Prostate cancer prognostic compositions and kits

ABSTRACT

Described herein are method, compositions and kits for prognosis of prostate cancer. The methods include determining the ratio of PCA3 and of a prostate-specific marker expression in a urine sample and correlating the value of the PCA3/prostate-specific marker ratio with the aggressiveness and mortality risk of prostate cancer in the subject. The method for prognosing prostate cancer in a sample of a patient includes assessing the amount of a prostate cancer specific PCA3 mRNA and the amount of prostate-specific marker in the sample; determining a ratio value of this amount of prostate cancer specific PCA3 mRNA over the amount of prostate-specific marker; comparing the ratio value to at least one predetermined cut-off value, wherein a ratio value above the predetermined cut-off value is indicative of a higher risk of mortality of prostate cancer as compared to a ratio value below the predetermined cut-off value.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a divisional of U.S. application Ser. No.14/745,955, filed Jun. 22, 2015, which is a continuation of U.S.application Ser. No. 13/914,303 filed Jun. 10, 2013, now U.S. Pat. No.9,096,907, which is a continuation of U.S. application Ser. No.13/571,124 filed Aug. 9, 2012, which is a continuation of U.S.application Ser. No. 13/101,440, now U.S. Pat. No. 8,257,924, which is acontinuation of U.S. application Ser. No. 11/794,048, now U.S. Pat. No.7,960,109, which is a 371 national stage of PCT application No. EP2005/014021 filed Dec. 23, 2005, which claims priority to U.S.provisional application No. 60/719,557 filed Sep. 23, 2005, and toCanadian application No. 2,491,067 filed Dec. 24, 2004. The patentapplications identified above are incorporated here by reference intheir entirety for all purposes.

SEQUENCE LISTING

This application contains a Sequence Listing in computer readable formentitled “01159-0007-05US_SeqListing.txt”, created Apr. 11, 2016, havinga size of 24.3 Kb. The computer readable form is incorporated herein byreference.

FIELD OF THE INVENTION

The present invention relates, in general, to prostate cancer. Morespecifically, the present invention relates not only to a method todetect but also to prognose and stage prostate cancer. The presentinvention relates to a staging and prognosis of prostate cancer bydetermining in a sample from a patient the ratio of mRNAs expressed inurinary sediments from patients. The invention further relates to theuse of ratios of prostatic mRNAs as a theranostic marker for prostatecancer. The present invention also relates to kits containing nucleicacid primers and kits containing nucleic acid primers and nucleic acidprobes to diagnose, stage, and prognose prostate cancer in a sample ofhuman afflicted with prostate cancer.

BACKGROUND OF THE INVENTION

Over the last decade, cancer of the prostate has become the mostcommonly diagnosed malignancy among men and the second leading cause ofmale cancer deaths in the western population, following lung cancer(Landis et al., 1998, CA Cancer J. Clin. 48(1):6-29). Of all cancers,the incidence of prostate cancer increases most rapidly with age. Aslongevity among the western population increases, there continues to bea corresponding rise in the number of prostate cancers with an expectedincrease of 60% in this decade alone. Mortality has increased at aslower rate, but overall has doubled in the last 50 years. Although thedisease is typically diagnosed in men over the age of 65, its impact isstill significant in that the average life span of a man who dies fromprostate cancer is reduced by 9-10 years. If discovered, early prostatecancer can now be cured with surgery in approximately 90% of cases.However, the disease is slowly fatal once the tumor spreads outside thearea of the gland and forms distant metastases. Early detection andaccurate staging are therefore of great importance for the accuratechoice of therapy and should improve the success rate of treatments andreduce the mortality rate associated with prostate cancer.

Despite many advances in recent years, the precision with which anindividual suffering from prostate cancer can be staged is stillsub-optimal. The main reason for this is the lack of very specific andsensitive molecular tests for accurate staging and the fact that tumorspread beyond the prostate is generally microscopic rather thanmacroscopic and are therefore difficult to detect. Digital rectalexamination of the prostate has been the cornerstone for the localstaging of prostatic cancer for many decades, but it oftentimesunderestimates the extent of the disease. Transrectal ultrasound byitself is only of limited value as a means of prostate cancer staging.Computer tomography and magnetic resonance imaging have generally beendisappointing in the staging of prostate cancer (Kirby, 1997, Prostatecancer and Prostatic Diseases 1:2-10). Recent promising approaches toprostate cancer staging imply the use of biochemical and moleculartechnologies, centered around proteins markers or their correspondingnucleic acids which are preferentially expressed in prostate cells(Lange, 1997, In “Principles and Practice of Genitourinary Oncology” ed.Lippincott-Raven Publishers, Ch. 41: 417-425).

Tumor markers are often found in a biological sample of cancer patientsat elevated concentrations compared to healthy people. These markers areoften proteins or nucleic acids encoding such proteins. Tumor markerscan also be non-coding nucleic acid molecules. They sometime have thepotential to be useful for staging, monitoring and follow up of tumorpatients.

The change of the tumor marker level, as well as its value compared toaverage healthy people has the potential to be used for monitoringcancer therapy. A persistent rise or a value above a defined cut-off canbe indicative of recurrent cancer or of a particular stage of cancer. Insome cases, tumor makers can also be used for screening personssuspected of having cancer, such tumor markers being often elevatedbefore the appearance of any clinical evidence of the disease.

The identification of tumor markers or antigens associated with prostatecancer has stimulated considerable interest because of their use inscreening, diagnosis, prognosis, clinical management and potentialtreatment of prostate cancer. Indeed, patients with locally confineddisease can often be cured by radical prostatectomy or radiationtherapy, but for patients with distantly spread disease no curativetreatment is available. This emphasizes the need for new prostate(cancer) specific therapeutic targets. Several genes have been describedthat are specifically expressed in the prostate, e.g., PSA (Sokoll etal., 1997, Prostate-specific antigen. Its discovery and biochemicalcharacteristics. Urol. Clin. North Am. 24:253-259) prostate-specificmembrane antigen (PSM: Fair et al., 1997, Prostate-specific membraneantigen. Prostate 32:140-148), prostate stem cell antigen (Reiter etal., 1998. Prostate stem cell antigen: a cell surface markeroverexpressed in prostate cancer. Proc. Natl. Acad. Sci. USA95:1735-1740), TMPRSS2 (Lin et al., 1999. Prostate-localized andandrogen-regulated expression of the membrane-bound serine proteaseTMPRSS2. Cancer Res. 59:4180-4184), PDEF (Oettgen et al., 2000. PDEF, anovel prostate epithelium-specific ets transcription factor, interactswith the androgen receptor and activates prostate-specific antigen geneexpression. J. Biol. Chem. 275:1216-1225), prostate-specific gene-1(Hemess, 2003. A novel human prostate-specific gene-1 (HPG-1): molecularcloning, sequencing, and its potential involvement in prostatecarcinogenesis. Cancer Res. 63:329-336), and even some non-coding RNA's(ncRNA's), like PCA3 (Bussemakers et al., 1999. DD3: a newprostate-specific gene, highly overexpressed in prostate cancer [CancerRes. 59:5975-5979], WO98/045420, WO01/023550, WO2004/070056,WO020051003387), PCGEM1 (Srikantan et al., 2000. PCGEM1, aprostate-specific gene, is overexpressed in prostate cancer. Proc. Natl.Acad. Sci. USA 97:12216-12221) and the gene cluster P704P, P712P, andP775P (Stolk et al., 2004. P704P,P712P, and P775P: A genomic cluster ofprostate-specific genes. Prostate 60:214-226). Only a fraction of thesegenes have been associated with prostate cancer prognosis, progressionand/or metastatic capacity and as having the potential to be valuabletherapeutic targets. The most notorious prostate tumor markers used forsurveillance, follow up, monitoring and choice of therapy for prostatecancer are PSA (prostate specific antigen) and PSM (prostate specificmembrane) antigen.

PSA is a serine protease encoded by the PSA gene located on chromosome19. This glycoprotein is expressed under androgen control by glandularepithelial cells of the prostate and secreted into seminal plasma toliquefy it. PSA protein is normally confined to the prostate but in thecase of prostatic disease such as cancer or BPH (benign prostatehyperplasia), PSA leaks into the blood where it is present in differentforms, including one that is and one that is not bound to proteincomplexes (El-Shirbiny, 1994, Adv. Clin. Chem. 31:99). The measurementof total PSA serum concentrations is one of the most frequently used andFDA approved biochemical tests in the screening and management ofprostate cancer patients. Studies to date have suggested that screeningwith PSA, in conjunction with digital rectal exams and transrectalultrasound, increases the detection of early prostate cancers oftenwhile still localized to the gland itself (Brawer et al., 1992, J. Urol.147:841). Serum PSA is also useful for monitoring of patients aftertherapy, especially after surgical prostatectomy. However, total PSAmeasurements also identify a large number of patients with abnormallyelevated levels who are subsequently found to have no prostate cancer.Recently, the concept of measuring the percentage free/total PSA ratiowas shown to increase the specificity of prostate cancer screening inmen with PSA between 4 and 10 ng/ml (Letran et al., 1998, J. Urol.160:426).

The PSM gene encodes a transmembrane glycoprotein expressed byepithelial cells of normal prostate, benign prostate hyperplasia and, toa greater extent, malignant prostatic tissue. Low levels of PSM are alsodetected in some other tissues (Israeli et al., 1994, Cancer Res.54:1807). PSA and PSM have also been targets for molecular approaches toprostate cancer using RT-PCR (reverse transcription-polymerase chainreaction). RT-PCR analyzes of blood, lymph nodes and bone marrow fromprostate cancer patients using PSA and PSM have disclosed the extremesensitivity of this approach. However, further investigations arerequired to establish the usefulness of PSM as a marker for prostaticcancer.

A new prostate cancer marker, PCA3, was discovered a few years ago bydifferential display analysis intended to highlight genes associatedwith prostate cancer development (PCT application number PCT/CA98/00346,and PCT application number PCT/CA00/01154). PCA3 is located onchromosome 9 and composed of four exons. It encodes at least fourdifferent transcripts which are generated by alternative splicing andpolyadenylation. By RT-PCR analysis, PCA3 expression was found to belimited to the prostate and absent in all other tissues, includingtestis, ovary, breast and bladder. Northern blot analysis showed thatPCA3 is highly expressed in the vast majority of prostate cancersexamined (47 out of 50) whereas no or very low expression is detected inbenign prostate hyperplasia or normal prostate cells from the samepatients. A search of the protein encoded by the putative ORF of PCA3,has yet to be successful. In addition, based on sequence analysis and invitro translation experiments no protein product was found for PCA3,therefore reinforcing the contention that PCA3 is a non-coding RNA(ncRNA). Thus, although, it is still possible that a polypeptide isencoded by PCA3 (and quickly degraded, processed, etc.), it stronglyappears that PCA3 is a ncRNA.

PCA3 would thus be the first non-coding RNA described in relation toprostate cancer. One thing which has been clearly demonstrated, however,is that PCA3 is the most prostate-cancer-specific gene identified todate. PCA3 is alternatively spliced and poly-adenylated andoverexpressed 50-500-fold in 95% of prostate cancer tissues and prostatecancer metastases in comparison to normal prostate tissues (de Kok etal., 2002. PCA3, a very sensitive and specific marker to detect prostatetumors. Cancer Res. 62:2695-2698; Hessels et al., 2003. PCA3-basedmolecular urine analysis for the diagnosis of prostate cancer. Eur.Urol. 44:8-16). No expression is detected in other normal or cancertissues.

The PCA3 gene is composed of 4 exons (e1-e4) and 3 introns (i1-i3).While PCA3 appears to be recognized as the best prostate-cancer markerever identified, this specificity has been contested in the literature.For example, Gandini et al., (Cancer Res. 2003; 63(15):4747) claim thatthe prostate-specific expression of PCA3 is restricted to that of exon 4of the PCA3 gene. However, the applicants have shown in a recent patentapplication that this is not the case (WO05/003387). There is at least20-fold overexpression of PCA3 in prostatic carcinomas in comparison tonormal or BPH tissues. Although PCA3 expression seems to increase withtumor grade and is detected in metastatic lesions, a true correlationbetween PCA3 expression and tumor grade has never been established.

In cancer research it is now well accepted that aggressiveness of canceris related to the degree of invasiveness of the cancer cell. Hundreds ofpapers have shown this. Even more, the molecular mechanisms associatedwith invasion and metastasis become more and more understood. However,these findings appeared restricted to the detection of cancer cellscirculating in the blood. The working hypothesis was that invasivecancer cells would migrate into the blood stream and that thus, thenumber of cancer cells in the circulation would be proportional to thedegree of invasiveness of a cancer. Whereas this concept gained a lot ofattention more than five years ago, experimental validation has stillnot been achieved. Thus the concept of measurement of cancer cells in abody fluid such as blood in particular, is still heavily debated.

With the introduction of highly sensitive amplification technologiessuch as PCR technology which can enable, in some conditions, as littleas the detection of a single tumor cell in a background of predominantlynormal cells, it became feasible to improve cancer diagnosis in bloodsamples. It is assumed that transcripts of epithelial cells do notnormally occur in the blood circulation. Therefore, the detection ofthese transcripts in the serum or plasma might indicate the presence ofdisseminated prostate cancer cells. In the last 12 years many reportshave been written on the RT-PCR-based detection of disseminated prostatecancer cells using PSA mRNA as a target. However, remarkable differenceswere observed in the sensitivity of the RT-PCR-based assays since theseassays were qualitative, not standardized, and difficult to reproduce invarious laboratories (Foster et al., 2004, Oncogene, 23, 5871-5879). Toenhance the sensitivity of these assays researchers used nested-PCR.Unfortunately, this led to the amplification of illegitimate transcripts(Smith et al., 1995, Prostate-specific antigen messenger RNA isexpressed in non-prostate cells: implications for detection ofmicrometastases [Cancer Res. 55: 2640-2644)]. These detected transcriptswere produced and secreted in low amounts by any normal cell in the bodylike normal blood cells or epithelial cells. As a result, PSA mRNAtranscripts were found in the serum of women and healthy controls (Henkeet al., 1997, Increased analytical sensitivity of RT-PCR of PSA mRNAdecreases diagnostic specificity of detection of prostatic cells inblood [Int. J. Cancer. 70: 52-56]). As such, these RT-PCR-based methodswere of limited value. New sensitive, quantitative, and morereproducible assays using exogenous internal standards for the detectionof PSA and hK2 mRNA transcripts overcame this problem (Ylikoski et al.,2002, Simultaneous quantification of prostate-specific antigen and humanglandular kallikrein 2 mRNA in blood samples from patients with prostatecancer and benign disease [Clin. Chem. 48: 1265-127]). However, anotherproblem arose using organ-specific as opposed to cancer-specifictranscripts such as PSA mRNA and hK2 mRNA. Indeed, PSA mRNA transcriptswere detected in the serum or plasma of men with and without prostatecancer after prostate biopsies, leading to a false-positive indicationfor the presence of a disseminated cancer cell (Moreno et al., 1997,Transrectal ultrasound-guided biopsy causes hematogenous disseminationof prostate cells as determined by RT-PCR [Urology 49: 515-520] andPolascik et al., 1999, Influence of sextant prostate needle biopsy orsurgery on the detection and harvest of intact circulating prostatecancer cells [J. Urol. 162: 749-752]). Thus, there remains a need toidentify truly, highly over-expressed and prostate cancer-specific geneswhich could be used in a quantitative amplification-based assay.

The first suggestion for the appearance of cancer cells in the duct (andthus in a glandular fluid) was provided by Hessel et al., 2003 (Eur.Urol. 44: 8-16). It still remains to be demonstrated whether therelative increase of the number of cancer cells in an organ willcorrelate with its invasiveness. There also remains a need to showwhether the increase in cancer cells in a glandular fluid wouldcorrelate with the increase in invasiveness of cancer cells in thatgland (e.g., prostate). There also remains to be determined whether suchinvasiveness would be reflected in the blood, the urine or another bodyfluid. Indeed, while the hypothesis that an increase of cancer cells inblood (when originating from glandular fluids) should correlate with thegrade of cancer has been proposed a long time ago, the clinicalvalidation of that hypothesis remains to be provided.

In view of the fact that prostate cancer remains a life threateningdisease reaching a significant portion of the male population, thereremains a need for efficient and rapid diagnosis, prognosis and/ortheranosis. The development of molecular tests for the accurate stagingenabling, amongst other things, the selection of an appropriate therapy,should improve survival rate. However, despite many advances in recentyears, the precision with which an individual suffering from prostatecancer can be staged is still sub-optimal. One of the drawbacks of usingPSA or PSM for prostate cancer staging is that these markers areexpressed in normal as well as in cancerous cells. In addition, poorlydifferentiated tumors may escape diagnosis since they tend to producesignificantly less PSA protein than less aggressive tumors. This is thecase for 10% of all prostate cancers.

There thus remains a need to provide a better test for the staging andprognosis of prostate cancer. There also remains a need to provide aprostate cancer test which is more specific and more reliable forprostate cancer detection, staging and treatment methods.

The present invention seeks to meet these and other needs.

The present description refers to a number of documents, the content ofwhich is herein incorporated by reference, in their entirety.

SUMMARY OF THE INVENTION

The present invention is based upon the discovery that the ratio of PCA3and a second prostate-specific marker, both expressed in a urine samplenot only establishes the presence, absence or predisposition to prostatecancer but also surprisingly, specifically and sensibly determines theaggressiveness of prostate cancer and the outcome of the disease.

In addition, it was unexpectedly discovered that the value of the ratioof PCA3 and a second prostate specific marker (e.g., PSA) could becorrelated with tumor volume. Since prognosis of individual patient withprostate carcinoma is correlated strongly with tumor volume, themolecular tests of the present invention are further validated asprognostic tools and demonstrate their accuracy in the prognosis of thedisease. Thus, more knowledgeable decisions can be made by theclinicians. For example, specific treatment regimen may be adapted toeach patient in order to more efficiently treat prostate cancer, basedon the value of the ratio that is determined. In one particularembodiment, this second prostate specific marker is PSA.

Thus, the present invention provides for the first time a case-controlstudy that directly demonstrates the association between the PCA3/PSAexpression ratio in a sample, tumor volume and the aggressiveness ofprostate cancer. More particularly, the present invention relates to thequantitative determination of the PCA3/PSA mRNA expression ratio in aurine sample as a marker for the staging and aggressiveness of prostatecancer.

Accordingly, the present invention relates to a method for diagnosisand/or prognosis of prostate cancer in a subject comprising: (a)determining the value of the ratio of PCA3/PSA mRNA expressed in asample; and (b) correlating the ratio with the presence or absence ofprostate cancer as well as the aggressiveness and mortality risk ofprostate cancer.

Herein the terms “diagnosis”, “diagnostic”, “diagnosing” and the like,as well known in the art, refer to an identification of prostate canceror to a predisposition of developing prostate cancer, based on adetection of at least one macromolecule (e.g., PCA3, PSA). The terms“prognosis”, “prognostic”, “prognosing” and the like, as well known inthe art, refer to the ability of predicting, forecasting or correlatinga given detection or measurement with a future outcome of prostatecancer of the patient (e.g., malignancy, likelihood of curing prostatecancer, survival, and the like). In accordance with one embodiment ofthe present invention, a measurement of the ratio of PCA3/PSA is adiagnosis or determination of tumor grade and/or tumor volume. Hence,based on the clinical knowledge of tumor grade and/or tumor volume, thisratio enables a prognosis of the disease (e.g., survival rate). Inanother embodiment a determination of the ratio over time enables apredicting of an outcome for the patient (e.g., increase or decrease inmalignancy, increase or decrease in grade of a prostatic tumor,likelihood of curing prostate cancer, survival, and the like).

By normal control ratio is meant a measured ratio of gene expressiondetected in a normal, healthy individual or in a population ofindividuals not suffering from prostate cancer. A normal individual isone with no clinical symptoms of prostate cancer. An increase in thePCA3/PSA ratio corresponds to an increase in the amount of PCA3 mRNAdetected, over the amount of PSA detected and positively correlates withmalignancy, tumor grade, tumor volume and negatively correlates withsurvival rate. In contrast, a decrease in the PCA3/PSA ratio correspondsto a decrease in the amount of PCA3 mRNA detected, over the amount ofPSA detected and correlates with a decrease in malignancy, tumor grade,or tumor volume and correlates with an increase in survival rate.

The present invention also relates to theranostic methods i.e., the useof the molecular test of the present invention to diagnose the disease,choose or adapt the correct or most appropriate treatment regimen and/ormonitor the patient response to therapy.

Thus, the present invention also relates to a method to detect, and morespecifically stage prostate cancer in a sample from a subject in orderto choose the appropriate therapy.

The methods of the invention can be performed in vitro, ex vivo or invivo. However, a most preferred method is a method carried out onbiological samples, in particular on urine samples, prostate tissueresections, prostate tissue biopsies, ejaculate or on bladder washings.

In one embodiment, the present invention features a method fordetermining prostate cancer prognosis in a subject comprising: (a)determining the value of the ratio of PCA3/second prostate-specificmRNAs expressed in a sample: and (b) correlating said PCA3/secondprostate-specific mRNAs ratio with the presence or absence of prostatecancer as well as the aggressiveness or mortality risk of prostatecancer. In one particular embodiment the second prostate-specific mRNAis PSA mRNA and the urine sample is obtained following digital rectalexamination (DRE).

In one particular embodiment, the present invention concerns a methodfor prognosing prostate cancer in a biological sample of a patientcomprising: (a) assessing the amount of a prostate cancer specific PCA3mRNA and the amount of PSA in the biological sample; (b) determining aratio value of the amount of prostate cancer specific PCA3 mRNA over theamount of PSA and (c) comparing the ratio value to at least onepredetermined cut-off value, wherein a ratio value above thepredetermined cut-off value is indicative of a higher risk of mortalityof prostate cancer as compared to a ratio value below the predeterminedcut-off value.

In another particular embodiment, the present invention relates to amethod for prognosing prostate cancer in a biological sample comprising:(a) contacting a biological sample with at least one oligonucleotidethat hybridizes to a prostate cancer specific PCA3 mRNA: (b) contactingthe biological sample with at least one oligonucleotide that hybridizesto a PSA mRNA; (c) determining the amount of PCA3 mRNA and the amount ofPSA mRNA present in the biological sample; (d) determining a ratio valueof the amount of PCA3 mRNA over the amount of PSA mRNA; and (e)comparing the ratio value of the amount of PCA3 mRNA over the amount ofPSA mRNA to at least one predetermined cut-off value, wherein a ratiovalue above the predetermined cut-off value is indicative of thepresence of a more aggressive cancer as compared to a ratio value belowthe predetermined cut-off value which is indicative of the presence of aless aggressive cancer.

In a further particular embodiment, the present invention relates to amethod for assessing prostate cancer tumor volume in a biological samplecomprising: (a) assessing the amount of a prostate cancer specific PCA3nucleic acid and the amount of PSA in a sample; (b) determining a ratiovalue of the amount of the prostate cancer specific PCA3 nucleic acidover the amount of PSA; and (c) comparing the ratio value to at leastone predetermined cut-off value, wherein a ratio value above thepredetermined cut-off value is indicative of a greater prostate cancertumor volume as compared to a ratio value below of the predeterminedcut-off value.

In an additional particular embodiment, the present invention relates toa method of monitoring prostate cancer tumor growth in a biologicalsample of a patient comprising: (a) assessing the amount of a prostatecancer specific PCA3 nucleic acid and the amount of PSA in thebiological sample at a first point of time; (b) determining a ratiovalue of the amount of the prostate cancer specific PCA3 nucleic acidover the amount of PSA; (c) repeating steps (a) and (b) using abiological sample from the patient at a subsequent point of time; and(d) comparing the ratio value obtained in step (b) with the ratio valueobtained in step (c), wherein a higher ratio value in step (c) comparedto the ratio value obtained in step (b) is indicative of the progressionof prostate cancer and of a greater tumor volume.

In an additional particular embodiment, the present invention relates toa method of monitoring the progression of prostate cancer in abiological sample comprising: (a) contacting a biological sample with atleast one oligonucleotide that hybridizes to a prostate cancer specificPCA3 nucleic acid; (b) contacting the biological sample with at leastone oligonucleotide that hybridizes to a PSA nucleic acid; (c)determining the amount of PCA3 nucleic acid and the amount of PSAnucleic acid present in the biological sample; (d) determining a ratiovalue of the amount of PCA3 nucleic acid over the amount of PSA nucleicacid; (e) repeating steps (a) to (d) in a subsequent point of time; and(f) comparing the ratio value obtained in step (d) with the ratio valueobtained in step (e), wherein a higher ratio value in step (e) comparedto the ratio value obtained in step (d) is indicative of the progressionof prostate cancer.

In yet another particular embodiment, the present invention relates to adiagnostic and prognostic kit for prostate cancer comprising at leastone container having disposed therein (a) at least one oligonudeotidethat hybridizes to a prostate cancer specific PCA3 nucleic acid selectedfrom the group consisting of (i) a nucleic acid sequence set forth inSEQ ID NO:1, (ii) a nucleic acid sequence set forth in SEQ ID NO:2,(iii) a nucleic acid sequence fully complementary to (i) or (ii) and(iv) a nucleic acid sequence that hybridizes under high stringencyconditions to the nucleic acid sequence in i, ii or iii: (b) at leastone oligonucleotide that hybridizes to a PSA nucleic acid selected fromthe group consisting of (i) a nucleic acid sequence set forth in SEQ IDNO:38, (ii) a nucleic acid sequence fully complementary to (i), (iii) anucleic acid sequence that hybridizes under high stringency condition tothe nucleic acid sequence in (i) or (ii); and (c) instructions fordetermining prostate cancer diagnosis and prognosis based on thedetection of a particular ratio of prostate cancer specific PCA3 nucleicacid level over PSA nucleic acid level.

Also, in one particular embodiment, the present invention relates to amethod of determining the risk of progression of prostate cancer aftertherapy comprising: (a) assessing the amount of a prostate cancerspecific PCA3 nucleic acid and the amount of PSA in a sample beforetherapy; (b) determining a ratio value of the amount of the prostatecancer specific PCA3 nucleic acid over the amount of PSA; (c) repeatingsteps (a) and (b) using a biological sample from the patient after thetherapy; and (d) comparing the ratio value obtained after therapy withthe ratio value obtained before therapy, wherein a higher ratio value inthe sample after therapy compared to the ratio value obtained before thetherapy is indicative of the progression of prostate cancer.

In addition, in one particular embodiment, the present invention relatesto a method of staging prostate cancer in a biological sample of apatient comprising: (a) assessing the amount of a prostate cancerspecific PCA3 nucleic acid and the amount of PSA in the biologicalsample; (b) determining a ratio value of the amount of the prostatecancer specific PCA3 nucleic acid over the amount of PSA; (c) comparingthe ratio value with at least one predetermined cut-off value; and (d)correlating a ratio value with a particular stage of prostate cancer,wherein a ratio value above the predetermined cut-off value indicates amore advanced stage of prostate cancer as compared to a ratio valuebelow the predetermined cut-off value, thereby staging prostate cancer.

In another one particular embodiment, the present invention relates to amethod for prognosing prostate cancer in a human patient, comprising:(a) performing an in vitro nucleic acid amplification assay on abiological sample of the patient or extract thereof using a first primerpair which is specific to a prostate cancer specific PCA3 nucleic acidsequence and a second primer pair which is specific to a PSA nucleicacid sequence; (b) quantifying the PCA3 nucleic acid sequence and thePSA nucleic acid sequence; and (c) calculating a normalized ratio ofPCA3 over PSA, wherein the ratio can be correlated to a PCA3 mRNA leveland a PSA mRNA level in the patient, wherein the normalized ratio ofPCA3 over PSA positively correlates with a grade or stage of prostatecancer.

Yet in another particular embodiment, the present invention relates to akit for prognosing prostate cancer in a patient comprising: (a) a firstprimer pair specific for amplifying a PCA3 nucleic acid associated withprostate cancer present in patient sample; (b) a second primer pairspecific for amplifying a PSA nucleic acid; (c) reagents enabling aquantitative detection of PCA3 and of PSA nucleic acid amplificationproducts when the PCA3 and second prostate-specific nucleic acidsequence at present; and (d) instructions for determining prostatecancer diagnosis and prognosis based on the detection of a particularratio of prostate cancer specific PCA3 nucleic acid level over PSAnucleic acid level.

In yet a further embodiment, serum levels of PSA protein are assessed inorder to make a preselection of the patients that further need aPCA3/PSA ratio testing. In one particular embodiment, a cut-off valuefor further testing of 3 ng/ml of serum PSA protein level is used. Ofcourse other serum PSA protein cut-off values may be used depending onthe particular requirements of the test (target sensitivity andspecificity). In addition, serum PSA mRNA levels could alternatively beused in accordance with the present invention in order to make thepreselection of the patients that need PCA3/PSA ratio testing.

In a related embodiment, the ratio of PCA3/PSA mRNAs expressed in asample is determined by detecting RNAs encoded by the PCA3 and PSA genesusing an amplification method. In a further embodiment, The RNAamplification method is coupled to real-time detection of the amplifiedproducts using fluorescence specific probes. In yet a furtherembodiment, the amplification method is PCR or RT-PCR. In an additionalembodiment, the RT-PCR is real-time RT-PCR or a related method enablingdetection in real time of the amplified products.

In another embodiment, RNAs encoded by the PCA3 and PSA genes aredetected in a nucleic acid extract by an in vitro RNA amplificationmethod named Nucleic Acid Based Amplification (NASBA). Of course otherRNA amplification methods are known and the instant methods and kits aretherefore not limited to NASBA. Non-limiting examples of such RNAamplification methods include transcriptase-mediated amplification(TMA), rolling circle amplification, strand displacement amplification(SDA) and ligase chain reaction (LCR).

In a further embodiment, the amplified products are detected in ahomogenous phase using a fluorescent probe. In one embodiment, theBeacon approach is used. In another embodiment, the products aredetected on solid phase using fluorescent or colorimetric method. Itshould thus be understood that numerous fluorescent, colorimetric orenzymatic methods can be used in accordance with the present inventionto detect and/or quantify RNAs. Other types of labelled probes andprimers or other types of detection methods may also be used in thepresent invention (e.g., hybridization assays such as Northern blots,dot blots or slot blots and radiolabelled probes and primers).

The amplification and/or detection of RNAs encoded by the PCA3 and PSAgenes to determine the level and ratio of expression of these RNAs in asample can be done simultaneously or separately. The biological samplecan be selected from the group consisting of prostate tissue resection,prostate tissue biopsies, ejaculates and bladder washings. Urine sampleobtained after digital rectal examination (DRE) are particularly useful.Of course, it should be understood that the present methods and kitscould also be used on a urine sample obtained without DRE, or on othertypes of samples such as sperm or mixed urine and sperm (e.g., firsturine sample following ejaculation), provided that the amplificationmethod and/or detection method is sensitive enough to detect thetargeted markers (PCA3 and second marker). Experiments showed that themethods and kits of the present invention could also be performed withthese types of samples.

In one embodiment, the RNAs encoded by the PCA3 and PSA genes areamplified from a cell contained in a voided urine sample from a subject.

In one embodiment, the cells collected from the urine sample areharvested and a total nucleic acid extraction is carried out. In oneparticular embodiment, total nucleic acid extraction is carried outusing a solid phase band method on silica beads as described by Boom etal., 1990 (J. Clin. Microbiol. 28: 495-503). In another embodiment, thenucleic acids are purified using another target capture method (seebelow). Of course, it should be understood that numerous nucleic acidextraction and purification methods exist and thus, that other methodscould be used in accordance with the present invention. Non-limitingexamples include a phenol/chloroform extraction method and targetcapture purification method (see below). Other such methods aredescribed in herein referenced textbooks. It should also be recognizedthat numerous means to stabilize or protect the prostate cells containedin the urine sample or other sample, as well as to stabilize or protectthe RNA present in these cells are well known in the art.

In another embodiment, the methods of the present invention are carriedout using a crude, unpurified, or semi-purified sample.

Although the determination of a PCA3/second prostate specific markerratio based on mRNA detection is preferred, the present invention is notso limited. For example, a ratio between PCA3 mRNA/second prostatespecific marker protein or polypeptide may well be used in accordancewith the present invention. The type of molecular entity (e.g., mRNA orpolypeptide) which is precisely detected can thus be adapted to suitparticular needs as long as the level of the macromolecule that isdetected is correlated with the transcriptional activity of the genefrom which it is derived.

In one particular embodiment, the present invention also relates to aprostate cancer theranostic, diagnostic and prognostic kit for detectingthe presence and amount of PCA3 and PSA nucleic acids in a sample. Suchkit generally comprises a first container means having disposed thereinat least one oligonucleotide probe and/or primer that hybridizes to aPCA3 and/or PSA nucleic acid (e.g., PCA3 RNA, PSA RNA) and a secondcontainer means containing at least one other oligonucleotide primerand/or probe that hybridizes to the above-mentioned PCA3 or PSA specificsequences. In another embodiment, a third container means containsprobes which specifically hybridizes to the PCA3 and PSA amplificationproducts. In a preferred embodiment, the kit further includes othercontainers comprising additional components such as an additionaloligonucleotide or primer and/or one or more of the following: buffers,reagents to be used in the assay (e.g., wash reagents, polymerases,internal controls (IC) or else) and reagents capable of detecting thepresence of bound nucleic acid probe(s)/primer(s). Of course numerousembodiments of the kits of the present invention are possible. Forexample, the different container means can be divided in amplifyingreagents and detection reagents. In one such an embodiment, a firstcontainer means contains amplification or hybridization reagentsspecific for the target nucleic acids of the present invention (e.g.,PCA3, PSA and/or internal control nucleic acids) and the secondcontainer means contains detection reagents. Alternatively, thedetection reagents and amplification reagents can be contained in thesame container means. Of course the separation or assembly of reagentsin same or different container means is dictated by the types ofextraction, amplification or hybridization methods, and detectionmethods used as well as other parameters including stability, need forpreservation, etc. In addition, the kits may further includeinstructions for practicing the diagnostic, theranostic and/orprognostic methods of the present invention. Such instructions canconcern details relating to the experimental protocol as well as to thecut-off values for the PCA3/second prostate specific marker ratio thatmay be used.

In a related aspect, the present invention features nucleic acids probesand primers for the specific detection of the presence of PCA3 and thesecond prostate-specific cancer marker (e.g., PSA) mRNAs in a sample.Also provided is an array of nucleic acids that binds to one or morePCA3/PSA nucleic acids

In one particular embodiment the present invention relates to kits andmethods for prognosing prostate cancer in a patient, based on adetermination of the ratio of PCA3/PSA using urinary sediments afterDRE, the ratio acting as a theranostic and prognostic marker, based onthe increase in the percentage of cancer cells in the urine followingthe DRE.

In one particular embodiment of the present invention the detection ofPCA3 is based on the targeting of exon 1 thereof, by one primer. In onesuch particular embodiment, primers on each side of intron 1 are used toamplify a portion of PCA3 exon 1 and exon 2 sequences (intron 1 is anapproximately 20 kb intron). Numerous examples of primer pairs can bedesigned from the PCA3 sequences of the present invention and, ofcourse, are not limited to exon 1.

Thus, the present invention demonstrates for the first time that theratio between PCA3 and a second prostate-specific cancer marker (e.g.,PSA) expression is not only diagnostically, but also prognostically andtheranostically useful. Of course the prognostic ratio of the presentinvention may be optionally employed in conjunction with other markersfor prostate cancer and neoplastic diseases such as urinary plasminogenactivator, urinary plasminogen activator receptor, plasminogen inhibitor1, p53, E-cadherin, PSM, VEGF, etc.

Moreover, to the inventors' knowledge, prior to present invention, therewas no teaching that described that in glandular fluids (for instancebreast or prostate) the number of cancer cells in the extrusioncorrelated with invasiveness of the cancer. In addition, there was noprior art that demonstrated or suggested that the ratio of PCA3 mRNAover a second prostate specific mRNA (e.g., PSA) would increase withtumor volume and aggressiveness of cancer and thus, that such a ratiocould be used as a theranostic, prognostic or staging marker. It isalleged herein that prior to the present invention it could not bepredicted whether aggressive cancer cells would migrate into the bloodstream or into the urine. The theranostic and prognostic value of theratio of the present invention is based on the demonstration of a numberof phenomenons, which had previously not been shown: (1) aggressiveprostate cancer cells are more invasive; (2) more invasive cells alsoare more capable of invading the prostatic acini; (3) the fraction ofcancer cells in the urinary sediment will therefore increase; (4) thusthe PCA3/second marker (e.g., PSA) mRNA ratio will increase; (5) tumorvolume is also correlated with the PCA3/second marker mRNA ratio; and(6) the modest increase in PCA3 with grade and the modest decrease onPSA mRNA may enhance this effect.

Thus, in accordance with the teachings of the present invention, oncethe ratio of PCA3/second marker (e.g., PSA) has been assessed, it ispossible to: (1) determine the presence, absence or predisposition todevelop prostate cancer; (2) if prostate cancer is detected, determinethe stage, tumor volume, tumor grade and agressivity of the cancer, (3)predict the outcome of the disease (prognosis); and (4) identify themost appropriate therapy for the patient.

In addition, one particular advantage of the present invention is theuse of a ratio of the present invention as a theranostic, diagnostic andprognosis tool. Although the particular value of the PCA3/second marker(e.g., PSA) ratio will vary depending on the second marker used (for agiven stage/grade/tumor volume), it is likely to vary only slightly withthe type of amplification/detection method (once a particularPCA3/second marker pair is chosen). Thus, as long as the methods usedfor determining the level of PCA3 and of the second marker arecomparable in terms of sensitivity and specificity, the value of theratio for given sample should be more or less the same (i.e. consideredstatistically similar in view of the variation in the chosen method).Therefore, once a pair of marker is chosen, various detection methodsmay be used interchangeably as long as that the methods are similarlyspecific and sensitive.

Unless defined otherwise, the scientific and technological terms andnomenclature used herein have the same meaning as commonly understood bya person of ordinary skill to which this invention pertains. Commonlyunderstood definitions of molecular biology terms can be found forexample in Dictionary of Microbiology and Molecular Biology, 2nd ed.(Singleton et al., 1994, John Wiley & Sons, New York, N.Y.) or TheHarper Collins Dictionary of Biology (Hale & Marham, 1991, HarperPerennial, New York, N.Y.), Rieger et al., Glossary of genetics:Classical and molecular, 5^(th) edition, Springer-Verlag, New-York,1991; Alberts et al., Molecular Biology of the Cell, 4^(th) edition,Garland science, New-York, 2002; and, Lewin, Genes VII, OxfordUniversity Press, New-York, 2000. Generally, the procedures of molecularbiology methods and the like are common methods used in the art. Suchstandard techniques can be found in reference manuals such as forexample Sambrook et al., (2000, Molecular Cloning—A Laboratory Manual,Third Edition, Cold Spring Harbor Laboratories); and Ausubel et al.,(1994, Current Protocols in Molecular Biology, John Wiley & Sons,New-York).

Further objects and advantages of the present invention will be clearfrom the description that follows.

DEFINITIONS

In the present description, a number of terms are extensively utilized.In order to provide a clear and consistent understanding of thespecification and claims, including the scope to be given such terms,the following definitions are provided.

Nucleotide sequences are presented herein by single strand, in the 5′ to3′ direction, from left to right, using the one-letter nucleotidesymbols as commonly used in the art and in accordance with therecommendations of the IUPAC-IUB Biochemical Nomenclature Commission.

The use of the word “a” or “an” when used in conjunction with the term“comprising” in the claims and/or the specification may mean “one” butit is also consistent with the meaning of “one or more”, “at least one”,and “one or more than one”.

Throughout this application, the term “about” is used to indicate that avalue includes the standard deviation of error for the device or methodbeing employed to determine the value. Routinely a 10% to 15% deviationpreferably 10% is within the scope of the term “about”.

The term “DNA” or “RNA” molecule or sequence (as well as sometimes theterm “oligonucleotide”) refers to a molecule comprised generally of thedeoxyribonucleotides adenine (A), guanine (G), thymine (T) and/orcytosine (C). In “RNA”, T is replaced by uracil (U).

The present description refers to a number of routinely used recombinantDNA (rDNA) technology terms. Nevertheless, definitions of selectedexamples of such rDNA terms are provided for clarity and consistency.

As used herein, “nucleic acid molecule” or “polynucleotides”, refers toa polymer of nucleotides. Non-limiting examples thereof include DNA(e.g., genomic DNA, cDNA), RNA molecules (e.g., mRNA) and chimerasthereof. The nucleic acid molecule can be obtained by cloning techniquesor synthesized. DNA can be double-stranded or single-stranded (codingstrand or non-coding strand [antisense]). Conventional ribonucleic acid(RNA) and deoxyribonucleic acid (DNA) are included in the term “nucleicacid” and polynucleotides as are analogs thereof. A nucleic acidbackbone may comprise a variety of linkages known in the art, includingone or more of sugar-phosphodiester linkages, peptide-nucleic acid bonds(referred to as “peptide nucleic acids” (PNA); Hydig-Hielsen et al., PCTInt'l Pub. No. WO 95/32305), phosphorothioate linkages,methylphosphonate linkages or combinations thereof. Sugar moieties ofthe nucleic acid may be ribose or deoxyribose, or similar compoundshaving known substitutions, e.g., 2′ methoxy substitutions (containing a2′-O-methylribofuranosyl moiety; see PCT No. WO 98/02582) and/or 2′halide substitutions. Nitrogenous bases may be conventional bases (A, G,C, T, U), known analogs thereof (e.g., inosine or others; see TheBiochemistry of the Nucleic Acids 5-36, Adams et al., ed., 11^(th) ed.,1992), or known derivatives of purine or pyrimidine bases (see, Cook,PCT Int'l Pub. No. WO 93/13121) or “abasic” residues in which thebackbone includes no nitrogenous base for one or more residues (Arnoldet al., U.S. Pat. No. 5,585,481). A nucleic acid may comprise onlyconventional sugars, bases and linkages, as found in RNA and DNA, or mayinclude both conventional components and substitutions (e.g.,conventional bases linked via a methoxy backbone, or a nucleic acidincluding conventional bases and one or more base analogs).

Isolated nucleic acid molecule. An “isolated nucleic acid molecule”, asis generally understood and used herein, refers to a polymer ofnucleotides, and includes, but should not limited to DNA and RNA. The“isolated” nucleic acid molecule is purified from its natural in vivostate, obtained by cloning or chemically synthesized.

The terminology “PCA3 nucleic acid” and “PSA nucleic acid” or “PCA3polynucleotides” and “PSA polynucleotides” refers to a native PCA3 orPSA nucleic acid sequence. In one embodiment, the PCA3 nucleic acid hasthe sequence as set forth in SEQ ID NOs:1 and 2. In a relatedembodiment, the PSA nucleic acid has the sequence as set forth in SEQ IDNO:38. In another embodiment, the PSA nucleic acid encodes a PSAprotein. In one particular embodiment, the PCA3 nucleic acid sequencewhich contains the predicted ORF, encodes a PCA3 polypeptide. In afurther embodiment, the PCA3 and PSA nucleic acids are a non-codingnucleic acid sequences. In yet a further embodiment, the PCA3 and PSAsequences which are targeted by the PCA3 and PSA sequences encompassedby the present invention, are natural PCA3 and PSA sequences found in asubject's sample.

The terminology “amplification pair” or “primer pair” refers herein to apair of oligonucleotides (oligos) of the present invention, which areselected to be used together in amplifying a selected nucleic acidsequence by one of a number of types of amplification processes. Anon-limiting examples of a primer pair for amplifying PSA is SEQ IDNos:36 and 37.

“Amplification” refers to any known in vitro procedure for obtainingmultiple copies (“amplicons”) of a target nucleic acid sequence or itscomplement or fragments thereof. In vitro amplification refers toproduction of an amplified nucleic acid that may contain less than thecomplete target region sequence or its complement. Known in vitroamplification methods include, e.g., transcription-mediatedamplification, replicase-mediated amplification, polymerase chainreaction (PCR) amplification, ligase chain reaction (LCR) amplificationand strand-displacement amplification (SDA including multiplestrand-displacement amplification method (MSDA)). Replicase-mediatedamplification uses self-replicating RNA molecules, and a replicase suchas Qβ-replicase (e.g., Kramer et al., U.S. Pat. No. 4,786,600). PCRamplification is well known and uses DNA polymerase, primers and thermalcycling to synthesize multiple copies of the two complementary strandsof DNA or cDNA (e.g., Mullis et al., U.S. Pat. Nos. 4,683,195,4,683,202, and 4,800,159). LCR amplification uses at least four separateoligonucleotides to amplify a target and its complementary strand byusing multiple cycles of hybridization, ligation, and denaturation(e.g., EP Pat. App. Pub. No. 0 320 308). SDA is a method in which aprimer contains a recognition site for a restriction endonuclease thatpermits the endonuclease to nick one strand of a hemimodified DNA duplexthat includes the target sequence, followed by amplification in a seriesof primer extension and strand displacement steps (e.g., Walker et al.,U.S. Pat. No. 5,422,252). Two other known strand-displacementamplification methods do not require endonuclease nicking (Dattagupta etal., U.S. Pat. No. 6,087,133 and U.S. Pat. No. 6,124,120 (MSDA)). Thoseskilled in the art will understand that the oligonucleotide primersequences of the present invention may be readily used in any in vitroamplification method based on primer extension by a polymerase. (seegenerally Kwoh et al., 1990, Am. Biotechnol. Lab. 8:14-25 and (Kwoh etal., 1989, Proc. Natl. Acad. Sci. USA 86, 1173-1177; Lizardi et al.,1988, BioTechnology 6:1197-1202; Malek et al., 1994, Methods Mol. Biol.,28:253-260; and Sambrook et al., 2000, Molecular Cloning—A LaboratoryManual, Third Edition, CSH Laboratories). As commonly known in the art,the oligos are designed to bind to a complementary sequence underselected conditions.

Agarose Gel Electrophoresis. The most commonly used technique (thoughnot the only one) for fractionating double stranded DNA is agarose gelelectrophoresis. The principle of this method is that DNA moleculesmigrate through the gel as though it were a sieve that retards themovement of the largest molecules to the greatest extent and themovement of the smallest molecules to the least extent. Note that thesmaller the DNA fragment, the greater the mobility under electrophoresisin the agarose gel.

The DNA fragments fractionated by agarose gel electrophoresis can bevisualized directly by a staining procedure if the number of fragmentsincluded in the pattern is small. In order to visualize a small subsetof these fragments, a methodology referred to as a hybridizationprocedure (e.g., Southern hybridization) can be applied.

“Nucleic acid hybridization” refers generally to the hybridization oftwo single-stranded nucleic acid molecules having complementary basesequences, which under appropriate conditions will form athermodynamically favored double-stranded structure. Examples ofhybridization conditions can be found in the two laboratory manualsreferred above (Sambrook et al., 2000, supra and Ausubel et al., 1994,supra, or further in Higgins and Hames (Eds.) “Nucleic acidhybridization, a practical approach” IRL Press Oxford, Washington D.C.,(1985)) and are commonly known in the art. In the case of ahybridization to a nitrocellulose filter (or other such support likenylon), as for example in the well known Southern blotting procedure, anitrocellulose filter can be incubated overnight at a temperaturerepresentative of the desired stringency condition (60-65° C. for highstringency, 50-60° C. for moderate stringency and 40-45° C. for lowstringency conditions) with a labeled probe in a solution containinghigh salt (6×SSC or 5×SSPE), 5×Denhardt's solution, 0.5% SDS, and 100μg/ml denatured carrier DNA (e.g., salmon sperm DNA). Thenon-specifically binding probe can then be washed off the filter byseveral washes in 0.2×SSC/0.1% SDS at a temperature which is selected inview of the desired stringency: room temperature (low stringency), 42°C. (moderate stringency) or 65° C. (high stringency). The salt and SDSconcentration of the washing solutions may also be adjusted toaccommodate for the desired stringency. The selected temperature andsalt concentration is based on the melting temperature (Tm) of the DNAhybrid. Of course, RNA-DNA hybrids can also be formed and detected. Insuch cases, the conditions of hybridization and washing can be adaptedaccording to well-known methods by the person of ordinary skill.Stringent conditions will be preferably used (Sambrook et al., 2000,supra). Other protocols or commercially available hybridization kits(e.g., ExpressHyb™ from BD Biosciences Clonetech) using differentannealing and washing solutions can also be used as well known in theart. As is well known, the length of the probe and the composition ofthe nucleic acid to be determined constitute further parameters of thehybridization conditions. Note that variations in the above conditionsmay be accomplished through the inclusion and/or substitution ofalternate blocking reagents used to suppress background in hybridizationexperiments. Typical blocking reagents include Denhardt's reagent,BLOTTO, heparin, denatured salmon sperm DNA, and commercially availableproprietary formulations. The inclusion of specific blocking reagentsmay require modification of the hybridization conditions describedabove, due to problems with compatibility. Hybridizing nucleic acidmolecules also comprise fragments of the above described molecules.Furthermore, nucleic acid molecules which hybridize with any of theaforementioned nucleic acid molecules also include complementaryfragments, derivatives and allelic variants of these molecules.Additionally, a hybridization complex refers to a complex between twonucleic acid sequences by virtue of the formation of hydrogen bondsbetween complementary G and C bases and between complementary A and Tbases; these hydrogen bonds may be further stabilized by base stackinginteractions. The two complementary nucleic acid sequences hydrogen bondin an antiparallel configuration. A hybridization complex may be formedin solution (e.g., Cot or Rot analysis) or between one nucleic acidsequence present in solution and another nucleic acid sequenceimmobilized on a solid support (e.g., membranes, filters, chips, pins orglass slides to which, e.g., cells have been fixed).

The terms complementary or complementarity refer to the natural bindingof polynucleotides under permissive salt and temperature conditions bybase-pairing. For example, the sequence “A-G-T” binds to thecomplementary sequence “T-C-A”. Complementarity between twosingle-stranded molecules may be “partial”, in which only some of thenucleic acids bind, or it may be complete when total complementarityexists between single-stranded molecules. The degree of complementaritybetween nucleic acid strands has significant effects on the efficiencyand strength of hybridization between nucleic acid strands. This is ofparticular importance in amplification reactions, which depend uponbinding between nucleic acids strands.

The term “hybridizes” as used in accordance with the present inventionmay relate to hybridizations under stringent or non-stringent conditionsas described herein above. The setting of conditions is well within theskill of the artisan and can be determined according to protocolsdescribed in the art. The term “hybridizing sequences” preferably refersto sequences which display a sequence identity of at least 40%,preferably at least 50%, more preferably at least 60%, even morepreferably at least 70%, particularly preferred at least 80%, moreparticularly preferred at least 90%, even more particularly preferred atleast 95% and most preferably at least 97% identity. Moreover, the term“hybridizing sequences” preferably refers to sequences encoding a PSAprotein having a sequence identity of at least 40%, preferably at least50%, more preferably at least 60%, even more preferably at least 70%,particularly preferred at least 80%, more particularly preferred atleast 90%, even more particularly preferred at least 95% and mostpreferably at least 97% identity with an amino acid sequence of a PSAprotein.

In accordance with the present invention, the term “identical” or“percent identity” in the context of two or more nucleic acid or aminoacid sequences, refers to two or more sequences or subsequences that arethe same, or that have a specified percentage of amino acid residues ornucleotides that are the same (e.g., 60% or 65% identity, preferably,70-95% identity, more preferably at least 95% identity), when comparedand aligned for maximum correspondence over a window of comparison, orover a designated region as measured using a sequence comparisonalgorithm as known in the art, or by manual alignment and visualinspection. Sequences having, for example, 60% to 95% or greatersequence identity are considered to be substantially identical. Such adefinition also applies to the complement of a test sequence. Preferablythe described identity exists over a region that is at least about 15 to25 amino acids or nucleotides in length, more preferably, over a regionthat is about 50 to 100 amino acids or nucleotides in length. Thosehaving skill in the art will know how to determine percent identitybetween/among sequences using, for example, algorithms such as thosebased on CLUSTALW computer program (Thompson Nucl. Acids Res. 2 (1994),4673-4680) or FASTDB (Brutlag Comp. App. Biosci. 6 (1990), 237-245), asknown in the art. Although the FASTDB algorithm typically does notconsider internal non-matching deletions or additions in sequences,i.e., gaps, in its calculation, this can be corrected manually to avoidan overestimation of the % identity. CLUSTALW, however, does takesequence gaps into account in its identity calculations. Also availableto those having skill in this art are the BLAST and BLAST 2.0 algorithms(Altschul Nucl. Acids Res. 25 (1977), 3389-3402). The BLASTN program fornucleic acid sequences uses as defaults a word length (W) of 11, anexpectation (E) of 10, M=5, N=4, and a comparison of both strands. Foramino acid sequences, the BLASTP program uses as defaults a wordlength(W) of 3, and an expectation (E) of 10. The BLOSUM62 scoring matrix(Henikoff Proc. Natl. Acad. Sci., USA, 89, (1989), 10915) usesalignments (B) of 50, expectation (E) of 10, M=5, N=4, and a comparisonof both strands. Moreover, the present invention also relates to nucleicacid molecules the sequence of which is degenerate in comparison withthe sequence of an above-described hybridizing molecule. When used inaccordance with the present invention the term “being degenerate as aresult of the genetic code” means that due to the redundancy of thegenetic code different nucleotide sequences code for the same aminoacid. The present invention also relates to nucleic acid molecules whichcomprise one or more mutations or deletions, and to nucleic acidmolecules which hybridize to one of the herein described nucleic acidmolecules, which show (a) mutation(s) or (a) deletion(s).

A “probe” is meant to include a nucleic acid oligomer that hybridizesspecifically to a target sequence in a nucleic acid or its complement,under conditions that promote hybridization, thereby allowing detectionof the target sequence or its amplified nucleic acid. Detection mayeither be direct (i.e., resulting from a probe hybridizing directly tothe target or amplified sequence) or indirect (i.e., resulting from aprobe hybridizing to an intermediate molecular structure that links theprobe to the target or amplified sequence). A probe's “target” generallyrefers to a sequence within an amplified nucleic acid sequence (i.e., asubset of the amplified sequence) that hybridizes specifically to atleast a portion of the probe sequence by standard hydrogen bonding or“base pairing.” Sequences that are “sufficiently complementary” allowstable hybridization of a probe sequence to a target sequence, even ifthe two sequences are not completely complementary. A probe may belabeled or unlabeled. A probe can be produced by molecular cloning of aspecific DNA sequence or it can also be synthesized. Numerous primersand probes which can be designed and used in the context of the presentinvention can be readily determined by a person of ordinary skill in theart to which the present invention pertains. Non-limiting examples ofprimers and probes are shown in Tables 2-4. A person skilled in the artcan design numerous other probes and primers based on the teachingsherein and the common general knowledge.

By “sufficiently complementary” is meant a contiguous nucleic acid basesequence that is capable of hybridizing to another sequence by hydrogenbonding between a series of complementary bases. Complementary basesequences may be complementary at each position in sequence by usingstandard base pairing (e.g., G:C, A:T or A:U pairing) or may contain oneor more residues (including abasic residues) that are not complementaryby using standard base pairing, but which allow the entire sequence tospecifically hybridize with another base sequence in appropriatehybridization conditions. Contiguous bases of an oligomer are preferablyat least about 80% (81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100%), more preferably at least about 90%complementary to the sequence to which the oligomer specificallyhybridizes. Appropriate hybridization conditions are well known to thoseskilled in the art, can be predicted readily based on sequencecomposition and conditions, or can be determined empirically by usingroutine testing (see Sambrook et al., Molecular Cloning, A LaboratoryManual, 2^(nd) ed. (Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y., 1989) at §§1.90-1.91, 7.37-7.57, 9.47-9.51 and11.47-11.57, particularly at §9.50-9.51, 11.12-11.13, 11.45-11.47 and11.55-11.57).

Nucleic acid sequences may be detected by using hybridization with acomplementary sequence (e.g., oligonucleotide probes) (see U.S. Pat. No.5,503,980 (Cantor), U.S. Pat. No. 5,202,231 (Drmanac et al.), U.S. Pat.No. 5,149,625 (Church et al.), U.S. Pat. No. 5,112,736 (Caldwell etal.), U.S. Pat. No. 5,068,176 (Vijg et al.), and U.S. Pat. No. 5,002,867(Macevicz)). Hybridization detection methods may use an array of probes(e.g., on a DNA chip) to provide sequence information about the targetnucleic acid which selectively hybridizes to an exactly complementaryprobe sequence in a set of four related probe sequences that differ onenucleotide (see U.S. Pat. Nos. 5,837,832 and 5,861,242 (Chee et al.)).

A detection step may use any of a variety of known methods to detect thepresence of nucleic acid by hybridization to a probe oligonucleotide.One specific example of a detection step uses a homogeneous detectionmethod such as described in detail previously in Arnold et al., ClinicalChemistry 35:1588-1594 (1989), and U.S. Pat. No. 5,658,737 (Nelson etal.), and U.S. Pat. Nos. 5,118,801 and 5,312,728 (Lizardi et al.).

The types of detection methods in which probes can be used includeSouthern blots (DNA detection), dot or slot blots (DNA, RNA), andNorthern blots (RNA detection). Labeled proteins could also be used todetect a particular nucleic acid sequence to which it binds (e.g.,protein detection by far western technology: Guichet et al., 1997,Nature 385(6616): 548-552; and Schwartz et al., 2001, EMBO 20(3):510-519). Other detection methods include kits containing reagents ofthe present invention on a dipstick setup and the like. Of course, itmight be preferable to use a detection method which is amenable toautomation. A non-limiting example thereof includes a chip or othersupport comprising one or more (e.g., an array) of different probes.

A “label” refers to a molecular moiety or compound that can be detectedor can lead to a detectable signal. A label is joined, directly orindirectly, to a nucleic acid probe or the nucleic acid to be detected(e.g., an amplified sequence). Direct labeling can occur through bondsor interactions that link the label to the nucleic acid (e.g., covalentbonds or non-covalent interactions), whereas indirect labeling can occurthrough the use of a “linker” or bridging moiety, such as additionaloligonucleotide(s), which is either directly or indirectly labeled.Bridging moieties may amplify a detectable signal. Labels can includeany detectable moiety (e.g., a radionuclide, ligand such as biotin oravidin, enzyme or enzyme substrate, reactive group, chromophore such asa dye or colored particle, luminescent compound including abioluminescent, phosphorescent or chemiluminescent compound, andfluorescent compound). Preferably, the label on a labeled probe isdetectable in a homogeneous assay system, i.e., in a mixture, the boundlabel exhibits a detectable change compared to an unbound label.

Other methods of labeling nucleic acids are known whereby a label isattached to a nucleic acid strand as it is fragmented, which is usefulfor labeling nucleic acids to be detected by hybridization to an arrayof immobilized DNA probes (e.g., see PCT No. PCT/IB99/02073).

A “homogeneous detectable label” refers to a label whose presence can bedetected in a homogeneous fashion based upon whether the labeled probeis hybridized to a target sequence. A homogeneous detectable label canbe detected without physically removing hybridized from unhybridizedforms of the labeled probe. Homogeneous detectable labels and methods ofdetecting them have been described in detail elsewhere (e.g., see U.S.Pat. Nos. 5,283,174, 5,656,207 and 5,658,737).

As used herein, “oligonucleotides” or “oligos” define a molecule havingtwo or more nucleotides (ribo or deoxyribonucleotides). The size of theoligo will be dictated by the particular situation and ultimately on theparticular use thereof and adapted accordingly by the person of ordinaryskill. An oligonucleotide can be synthesized chemically or derived bycloning according to well-known methods. While they are usually in asingle-stranded form, they can be in a double-stranded form and evencontain a “regulatory region”. They can contain natural rare orsynthetic nucleotides. They can be designed to enhance a chosen criterialike stability for example. Chimeras of deoxyribonucleotides andribonucleotides may also be within the scope of the present invention.

Sequence Amplification. A method for generating large amounts of atarget sequence. In general, one or more amplification primers areannealed to a nucleic acid sequence. Using appropriate enzymes,sequences found adjacent to, or in between the primers are amplified.

As used herein, a “primer” defines an oligonucleotide which is capableof annealing to a target sequence, thereby creating a double strandedregion which can serve as an initiation point for nucleic acid synthesisunder suitable conditions. Primers can be, for example, designed to bespecific for certain alleles so as to be used in an allele-specificamplification system. For example, a primer can be designed so as to becomplementary to a short PCA3 RNA which is associated with a malignantstate of the prostate, whereas a long PCA3 RNA is associated with anon-malignant state (benign) thereof (PCT/CA00/01154 published under No.WO 01/23550). The primer's 5′ region may be non-complementary to thetarget nucleic acid sequence and include additional bases, such as apromoter sequence (which is referred to as a “promoter primer”). Thoseskilled in the art will appreciate that any oligomer that can functionas a primer can be modified to include a 5′ promoter sequence, and thusfunction as a promoter primer. Similarly, any promoter primer can serveas a primer, independent of its functional promoter sequence. Of coursethe design of a primer from a known nucleic acid sequence is well knownin the art. As for the oligos, it can comprise a number of types ofdifferent nucleotides. Skilled artisans can easily assess thespecificity of selected primers and probes (e.g., PSA, PCA3, controlsequences, etc. . . . ) by performing computer alignments/searches usingwell-known databases (e.g., Genbank™).

Amplification Primer. An oligonucleotide which is capable of annealingadjacent to a target sequence and serving as an initiation point for DNAsynthesis when placed under conditions in which synthesis of a primerextension product which is complementary to a nucleic acid strand isinitiated.

NASBA. Nucleic Acid Sequence Based Amplification (NASBA) can be carriedout in accordance with known techniques (Malek et al., Methods Mol Biol,28:253-260, U.S. Pat. Nos. 5,399,491 and 5,554,516). In an embodiment,the NASBA amplification starts with the annealing of an antisense primerP1 (containing the T7 RNA polymerase promoter) to the mRNA target.Reverse transcriptase (RTase) then synthesizes a complementary DNAstrand. The double stranded DNA/RNA hybrid is recognized by RNase H thatdigests the RNA strand, leaving a single-stranded DNA molecule to whichthe sense primer P2 can bind. P2 serves as an anchor to the RTase thatsynthesizes a second DNA strand. The resulting double-stranded DNA has afunctional T7 RNA polymerase promoter recognized by the respectiveenzyme. The NASBA reaction can then enter in the phase of cyclicamplification comprising six steps: (1) Synthesis of short antisensesingle-stranded RNA molecules (10¹ to 10³ copies per DNA template) bythe T7 RNA polymerase; (2) annealing of primer P2 to these RNAmolecules; (3) synthesis of a complementary DNA strand by RTase; (4)digestion of the RNA strand in the DNA/RNA hybrid; (5) annealing ofprimer P1 to the single-stranded DNA; and (6) generation of doublestranded DNA molecules by RTase. Because the NASBA reaction isisothermal (41° C.), specific amplification of ssRNA is possible ifdenaturation of dsDNA is prevented in the sample preparation procedure.It is thus possible to pick up RNA in a dsDNA background without gettingfalse positive results caused by genomic dsDNA.

Polymerase chain reaction (PCR). Polymerase chain reaction can becarried out in accordance with known techniques. See, e.g., U.S. Pat.Nos. 4,683,195; 4,683,202; 4,800,159; and 4,965,188 (the disclosures ofall three U.S. Patent are incorporated herein by reference). In general,PCR involves, a treatment of a nucleic acid sample (e.g., in thepresence of a heat stable DNA polymerase) under hybridizing conditions,with one oligonucleotide primer for each strand of the specific sequenceto be detected. An extension product of each primer which is synthesizedis complementary to each of the two nucleic acid strands, with theprimers sufficiently complementary to each strand of the specificsequence to hybridize therewith. The extension product synthesized fromeach primer can also serve as a template for further synthesis ofextension products using the same primers. Following a sufficient numberof rounds of synthesis of extension products, the sample is analyzed toassess whether the sequence or sequences to be detected are present.Detection of the amplified sequence may be carried out by visualizationfollowing Ethidium Bromide (EtBr) staining of the DNA following gelelectrophoresis, or using a detectable label in accordance with knowntechniques, and the like. For a review on PCR techniques (see PCRProtocols, A Guide to Methods and Amplifications, Michael et al., Eds,Acad. Press, 1990).

Ligase chain reaction (LCR) can be carried out in accordance with knowntechniques (Weiss, 1991, Science 264:1292). Adaptation of the protocolto meet the desired needs can be carried out by a person of ordinaryskill. Strand displacement amplification (SDA) is also carried out inaccordance with known techniques or adaptations thereof to meet theparticular needs (Walker et al., 1992, Proc. Natl. Acad. Sci. USA89:392-396; and ibid, 1992, Nucleic Acids Res. 20:1691-1696).

Target capture. In one embodiment, target capture is included in themethod to increase the concentration or purity of the target nucleicacid before in vitro amplification. Preferably, target capture involvesa relatively simple method of hybridizing and isolating the targetnucleic acid, as described in detail elsewhere (e.g., see U.S. Pat. Nos.6,110,678, 6,280,952, and 6,534,273). Generally speaking, target capturecan be divided in two family, sequence specific and non-sequencespecific. In the non-specific method, a reagent (e.g., silica beads) isused to capture non specifically nucleic acids. In the sequence specificmethod an oligonucleotide attached to a solid support is contacted witha mixture containing the target nucleic acid under appropriatehybridization conditions to allow the target nucleic acid to be attachedto the solid support to allow purification of the target from othersample components. Target capture may result from direct hybridizationbetween the target nucleic acid and an oligonucleotide attached to thesolid support, but preferably results from indirect hybridization withan oligonucleotide that forms a hybridization complex that links thetarget nucleic acid to the oligonucleotide on the solid support. Thesolid support is preferably a particle that can be separated from thesolution, more preferably a paramagnetic particle that can be retrievedby applying a magnetic field to the vessel. After separation, the targetnucleic acid linked to the solid support is washed and amplified whenthe target sequence is contacted with appropriate primers, substratesand enzymes in an in vitro amplification reaction.

Generally, capture oligomer sequences include a sequence thatspecifically binds to the target sequence, when the capture method isindeed specific, and a “tail” sequence that links the complex to animmobilized sequence by hybridization. That is, the capture oligomerincludes a sequence that binds specifically to its PCA3, PSA or toanother prostate specific marker (e.g., hK2/KLK2, PMSA, transglutaminase4, acid phosphatase, PCGEM1) target sequence and a covalently attached3′ tail sequence (e.g., a homopolymer complementary to an immobilizedhomopolymer sequence). The tail sequence which is, for example, 5 to 50nucleotides long, hybridizes to the immobilized sequence to link thetarget-containing complex to the solid support and thus purify thehybridized target nucleic acid from other sample components. A captureoligomer may use any backbone linkage, but some embodiments include oneor more 2′-methoxy linkages. Of course, other capture methods are wellknown in the art. The capture method on the cap structure (Edery et al.,1988, gene 74(2): 517-525, U.S. Pat. No. 5,219,989) and the silica-basedmethod are two non-limiting examples of capture methods.

An “immobilized probe” or “immobilized nucleic acid” refers to a nucleicacid that joins, directly or indirectly, a capture oligomer to a solidsupport. An immobilized probe is an oligomer joined to a solid supportthat facilitates separation of bound target sequence from unboundmaterial in a sample. Any known solid support may be used, such asmatrices and particles free in solution, made of any known material(e.g., nitrocellulose, nylon, glass, polyacrylate, mixed polymers,polystyrene, silane polypropylene and metal particles, preferablyparamagnetic particles). Preferred supports are monodisperseparamagnetic spheres (i.e., uniform in size ±about 5%), therebyproviding consistent results, to which an immobilized probe is stablyjoined directly (e.g., via a direct covalent linkage, chelation, orionic interaction), or indirectly (e.g., via one or more linkers),permitting hybridization to another nucleic acid in solution.

Complementary DNA (cDNA). Recombinant nucleic acid molecules synthesizedby reverse transcription of messenger RNA (“RNA”).

As used herein, the term “purified” refers to a molecule (e.g., nucleicacid) having been separated from a component of the composition in whichit was originally present. Thus, for example, a “purified nucleic acid”has been purified to a level not found in nature. A “substantially pure”molecule is a molecule that is lacking in most other components (e.g.,30, 40, 50, 60, 70, 75, 80, 85, 90, 95, 96, 97, 98, 99, 100% free ofcontaminants). By opposition, the term “crude” means molecules that havenot been separated from the components of the original composition inwhich it was present. For the sake of brevity, the units (e.g., 66, 67 .. . 81, 82, 83, 84, 85, . . . 91, 92% . . . . ) have not beenspecifically recited but are considered nevertheless within the scope ofthe present invention.

The terminology “prognosis”, “staging” and “determination ofaggressiveness” are defined herein as the prediction of the degree ofseverity of the prostate cancer and of its evolution as well as theprospect of recovery as anticipated from usual course of the disease.According to the present invention, once the aggressiveness of theprostate cancer has been determined appropriate methods of treatmentscan be chosen.

Herein the terminology “Gleason Score”, as well known in the art, is themost commonly used system for the grading/staging and prognosis ofadenocarcinoma. The system describes a score between 2 and 10, with 2being the least aggressive and 10 being the most aggressive. The scoreis the sum of the two most common patterns (grade 1-5) of tumor growthfound. To be counted a pattern (grade) needs to occupy more than 5% ofthe biopsy specimen. The scoring system requires biopsy material (corebiopsy or operative specimens) in order to be accurate; cytologicalpreparations cannot be used.

The “Gleason Grade” is the most commonly used prostate cancer gradingsystem. It involves assigning numbers to cancerous prostate tissue,ranging from 1 through 5, based on how much the arrangement of thecancer cells mimics the way normal prostate cells form glands. Twogrades are assigned to the most common patterns of cells that appear;these two grades (they can be the same or different): are then addedtogether to determine the Gleason score (a number from 1 to 10).

The Gleason system is based exclusively on the architectural pattern ofthe glands of the prostate tumor. It evaluates how effectively the cellsof any particular cancer are able to structure themselves into glandsresembling those of the normal prostate. The ability of a tumor to mimicnormal gland architecture is called its differentiation, and experiencehas shown that a tumor whose structure is nearly normal (welldifferentiated) will probably have a biological behavior relativelyclose to normal, i.e. that is not very aggressively malignant.

The principle is fairly simple, a Gleason grading from very welldifferentiated (grade 1) to very poorly differentiated (grade 5) isusually done for the most part by viewing the low magnificationmicroscopic image of the cancer. There are important additional detailswhich require higher magnification, and an ability to accurately gradeany tumor is achieved only through much training and experience inpathology.

Gleason Grades 1 and 2: These two grades closely resemble normalprostate. They are the least important grades because they seldom occurin the general population and because they confer a prognostic benefitwhich is only slightly better than grade 3. Both of these grades arecomposed by mass; in grade 2 they are more loosely aggregated, and someglands wander (invade) into the surrounding muscle (stroma).

Gleason Grade 3: This is the most common grade by far and is alsoconsidered well differentiated (like grades 1 and 2). This is becauseall three grades have a normal “gland unit” like that of a normalprostate; that is, every cell is part of a circular row which forms thelining of a central space (the lumen). The lumen contains prostaticsecretion like normal prostate, and each gland unit is surrounded byprostate muscle which keeps the gland units apart. In contrast to grade2, wandering of glands (invading) into the stroma (muscle) is veryprominent and is the main defining feature. The cells are dark ratherthan pale and the glands often have more variable shapes

Gleason Grade 4: This is probably the most important grade because it isfairly common and because of the fact that if a lot of it is present,patient prognosis is usually (but not always) worsened by a considerabledegree. Here also there is a big jump in loss of architecture. For thefirst time, disruption and loss of the normal gland unit is observed. Infact, grade 4 is identified almost entirely by loss of the ability toform individual, separate gland units, each with its separate lumen(secretory space). This important distinction is simple in concept butcomplex in practice. The reason is that there are a variety ofdifferent-appearing ways in which the cancers effort to form gland unitscan be distorted. Each cancer has its own partial set of tools withwhich it builds part of the normal structure. Grade 4 is like thebranches of a large tree, reaching in a number of directions from the(well differentiated) trunk of grades 1, 2, and 3. Much experience isrequired for this diagnosis, and not all patterns are easilydistinguished from grade 3. This is the main class of poorlydifferentiated prostate cancer, and its distinction from grade 3 is themost commonly important grading decision.

Gleason Grade 5: Gleason grade 5 is an important grade because itusually predicts another significant step towards poor prognosis. Itsoverall importance for the general population is reduced by the factthat it is less common than grade 4, and it is seldom seen in men whoseprostate cancer is diagnosed early in its development. This grade tooshows a variety of patterns, all of which demonstrate no evidence of anyattempt to form gland units. This grade is often calledundifferentiated, because its features are not significantlydistinguishing to make it look any different from undifferentiatedcancers which occur in other organs.

When a pathologist looks at prostate cancer specimens under themicroscope and gives them a Gleason grade, an attempt to identify twoarchitectural patterns and assign a Gleason grade to each one is made.There may be a primary or most common pattern and then a secondary orsecond most common pattern which the pathologist will seek to describefor each specimen; alternatively, there may often be only a single puregrade.

In developing his system, Dr. Gleason discovered that by giving acombination of the grades of the two most common patterns he could seein any particular patient's specimens, that he was better able topredict the likelihood that a particular patient would do well or badly.Therefore, although it may seem confusing, the Gleason score which aphysician usually gives to a patient, is actually a combination or sumof two numbers which is accurate enough to be very widely used. Thesecombined Gleason sums or scores may be determined as follows:

-   -   The lowest possible Gleason score is 2 (1+1), where both the        primary and secondary patterns have a Gleason grade of 1 and        therefore when added together their combined sum is 2.    -   Very typical Gleason scores might be 5 (2+3), where the primary        pattern has a Gleason grade of 2 and the secondary pattern has a        grade of 3, or 6 (3+3), a pure pattern.    -   Another typical Gleason score might be 7 (4+3), where the        primary pattern has a Gleason grade of 4 and the secondary        pattern has a grade of 3.    -   Finally, the highest possible Gleason score is 10 (5+5), when        the primary and secondary patterns both have the most disordered        Gleason grades of 5.

Another way of staging prostate cancer is by using the TNM System. Itdescribes the extent of the primary tumor (T stage), the absence orpresence of spread to nearby lymph nodes (N stage) and the absence orpresence of distant spread, or metastasis (M stage). Each category ofthe TNM classification is divided into subcategories representative ofits particular state. For example, primary tumors (T stage) may beclassified into:

-   -   T1: The tumor cannot be felt during a digital rectal exam, or        seen by imaging studies, but cancer cells are found in a biopsy        specimen;    -   T2: The tumor can be felt during a DRE and the cancer is        confined within the prostate gland;    -   T3: The tumor has extended through the prostatic capsule (a        layer of fibrous tissue surrounding the prostate gland) and/or        to the seminal vesicles (two small sacs next to the prostate        that store semen), but no other organs are affected;    -   T4: The tumor has spread or attached to tissues next to the        prostate (other than the seminal vesicles).

Lymph node involvement is divided into the following 4 categories:

-   -   N0: Cancer has not spread to any lymph nodes;    -   N1: Cancer has spread to a single regional lymph node (inside        the pelvis) and is not larger than 2 centimeters;    -   N2: Cancer has spread to one or more regional lymph nodes and is        larger than 2 centimeters, but not larger than 5 centimeters;        and    -   N3: Cancer has spread to a lymph node and is larger than 5        centimeters (2 inches).    -   Metastasis is generally divided into the following two        categories:    -   M0: The cancer has not metastasized (spread) beyond the regional        lymph nodes; and    -   M1: The cancer has metastasized to distant lymph nodes (outside        of the pelvis), bones, or other distant organs such as lungs,        liver, or brain.

In addition, the Tstage is further divided into subcategories T1a-cT2a-c, T3a-c and T4a-b. The characteristics of each of thesesubcategories are well known in the art and can be found in a number oftextbooks.

As used herein the terminology “prostate specific marker” relates to anymolecule whose presence in the sample indicates that such samplecontains prostate cells (or a marker therefrom). Therefore a “prostatespecific sequence” refers to a nucleic acid or protein sequencespecifically found in prostate cells and usually not in other tissueswhich could “contaminate” a particular sample. For certainty, when aurine sample is used, the second prostate specific marker according tothe present invention does not have to be solely expressed in theprostate. In fact markers which are solely expressed in one organ ortissue is very rare. However, should the second prostate specific markerbe expressed in non-prostate tissue, this non-prostate tissue expressionwill not jeopardized the specificity of this second marker provided thatit occurs in cells of tissues or organs which are not normally presentin the urine sample. Thus, when urine is the sample, this secondprostate-specific marker is not normally expressed in other types ofcells (e.g., cells from the urinary tract system) to be found in theurine sample. Similarly, if another type of sample is used (e.g., spermsample), the second prostate specific marker should not be expressed inother cell types that are normally encountered within such sample.

Control sample. By the term “control sample” or “normal sample” is meanthere a sample that does not contain a specifically chosen cancer. In aparticular embodiment, the control sample does not contain prostatecancer or is indicative of the absence of prostate cancer. Controlsamples can be obtained from patients/individuals not afflicted withprostate cancer. Other types of control samples may also be used. Forexample, a prostate specific marker can be used as to make sure that thesample contains prostate specific cells (this marker is generallydescribed herein as the second prostate-specific marker). In a relatedaspect, a control reaction may be designed to control the method itself(e.g., The cell extraction, the capture, the amplification reaction ordetection method, number of cells present in the sample, a combinationthereof or any step which could be monitored to positively validate thatthe absence of a signal (e.g., the absence of PCA3 signal) is not theresult of a defect in one or more of the steps). Once a cut-off value isdetermined, a control sample giving a signal characteristic of thepredetermined cut-off value can also be designed and used in the methodsof the present invention. Diagnosis/prognosis tests are commonlycharacterized by the following 4 performance indicators: sensitivity(Se), specificity (Sp), positive predictive value (PPV), and negativepredictive value (NPV). The following table presents the data used incalculating the 4 performance indicators.

TABLE 1 Disease/condition Presence (+) Absence (−) Test (+) A b a + b(−) C d c + d A + c a + b

Sensitivity corresponds to the proportion of subjects having a positivediagnostic test who truly have the disease or condition (Se=a/a+c).Specificity relates to the proportion of subjects having a negativediagnostic test and who do not have the disease or condition (Sp=d/b+d).The positive predictive value concerns the probability of actuallyhaving the disease or condition (e.g., lung cancer) when the diagnostictest is positive (PPV=a/a+b). Finally, the negative predictive value isindicative of the probability of truly not having the disease/conditionwhen the diagnostic test is negative (NPV=c/c+d). The values aregenerally expressed in %. Se and Sp generally relate to the precision ofthe test, while PPV and NPV concern its clinical utility.

Cut-off value (threshold). The cut-off value for the predisposition orpresence of prostate cancer is defined from a population of patientswithout prostate cancer as the average signal of PCA3 polynucleotides orfragments thereof divided by the average signal of a second prostatespecific marker (e.g., PSA) polynucleotides, polypeptides or fragmentsthereof plus n standard deviations (or average mean signal thereof).Cut-off values indicative of the presence or predisposition to developprostate cancer may be the same or alternatively, they may be differentvalues. Since tumor markers are in many instances not solely produced bytumor cells, deriving clinical utility from a given marker often entailsfinding a balance between sensitivity and specificity. Such a compromiseis often reached at a specific threshold

cut-off

value, which is empirically based on collected data. It should thus beunderstood that a person skilled in the art, to which the presentinvention pertains, will be able, with routine experimentation, toselect a particular cut-off value based on the desired specificity andsensitivity, the type of sample used, the preparation thereof, the stageof the cancer, the fact that a ratio is used rather than an absolutelevel of expression of PCA3, and other such factors described herein.More specifically, in the PCA3 case, the person of skill in the art canchoose the cut-off value to be higher or lower than the exemplifiedratio values of 132×10⁻³ and 200×10⁻³ described herein. Withoutspecifically listing all useful lower and higher values which can beselected for PCA3/PSA, and which are within the scope of the presentinvention, it should be understood that for example a normalized ratioof 100×10⁻³, 150×10⁻³, 175×10⁻³ or 250×10⁻³ could be selected by theskilled artisan in order to choose a useful level of specificity andsensitivity. In addition, when assessing serum PSA protein level acut-off other than the 3 ng/ml value exemplified herein can be used inaccordance with the present invention. For example, a cut-off value of 5ng/ml, 10 ng/ml, etc. may be used in accordance with the presentinvention when a preselection of the samples that further need PCA3/PCAratio testing is optionally made. Cut-off values for staging ordetermining the aggressiveness (prognosing) of prostate cancer aredefined from a population of patient having prostate cancer of differentstages or of different aggressiveness (Gleason score) as the averagesignal of PCA3 polynucleotides or fragments thereof divided by theaverage signal for a second prostate specific marker (e.g., PSA)polynucleotides, polypeptides or fragments thereof plus n standarddeviations (or average mean signal thereof) for a specific stage ofprostate cancer. Depending on the desired specificity and sensitivity ofthe test and on the particular stage, grade or volume of prostate tumorto be detected, a particular cut-off value will be chosen.

The terminologies “level” and “amount” are used herein interchangeablywhen referring to PCA3, PSA or other marker which is measured.

It should be understood by a person of ordinary skill, that numerousstatistical methods can be used in the context of the present inventionto determine if the test is positive or negative or to determine theparticular stage, grade, volume of the prostate tumor or aggressivitythereof.

Variant. The term “variant” refers herein to a protein or nucleic acidmolecule which is substantially similar in structure and biologicalactivity to the protein or nucleic acid of the present invention, tomaintain at least one of its biological activities. Thus, provided thattwo molecules possess a common activity and can substitute for eachother, they are considered variants as that term is used herein even ifthe composition, or secondary, tertiary or quaternary structure of onemolecule is not identical to that found in the other, or if the aminoacid sequence or nucleotide sequence is not identical.

A “biological sample” or “sample of a patient” is meant to include anytissue or material derived from a living or dead human which may containthe PCA3 and PSA target nucleic acids. Samples include, for example, anytissue or material that may contain cells specific for the PCA3 and PSAtargets (or other specific prostate marker) such as prostate biopsy,urine, semen, bladder washings or other body fluids, tissues ormaterials. The preferred sample according to the present invention is aurine sample following digital rectal examination (or other means whichincrease the content of prostate cells in urine). The biological samplemay be treated to physically disrupt tissue or cell structure, thusreleasing intracellular components into a solution which may furthercontain enzymes, buffers, salts, detergents, and the like which are usedto prepare the sample for analysis. In one particular embodiment thesample is a urine sample following a DRE.

Other objects, advantages and features of the present invention willbecome more apparent upon reading of the following non-restrictivedescription of preferred embodiments thereof, given by way of exampleonly with reference to the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

Having thus generally described the invention, reference will now bemade to the accompanying drawings, showing by way of illustration apreferred embodiment thereof and in which:

FIG. 1 shows one embodiment of an assay principle of the presentinvention.

FIGS. 2A-2B show a gene-based PCA3-analysis of urinary sediments afterextended DRE. FIG. 2A shows a plot of sensitivity over specificity.Urinary sediments were obtained after extended DRE from a cohort of 108men with serum PSA levels >3 ng/ml. The diagnostic efficacy of thePCA3-based assay of urinary sediments is visualized by a ReceiverOperating Characteristic (ROC) curve. Based on this ROC curve, a cut-offlevel of 200.10-3 was determined. FIG. 2B shows the PCA3/PSA valuesobtained from the urinary sediments of FIG. 2A, but summarized in abox-plot. The median PCA3/PSA value (thick black horizontal line),outliers (open circles) and extremes (stars) are shown. The cut-offvalue is indicated by a dashed line.

FIG. 3 shows the prognostic significance of PCA3/PSA. Urinary sedimentswere obtained after extended DRE from a new cohort of 136 men with serumPSA levels >3 ng/ml. In a box-plot the PCA3/PSA values obtained fromthese urinary sediments were correlated with Gleason score. The medianPCA3/PSA value (thick black horizontal line), outliers (open circles)and extremes (stars) are shown. Because of minor adjustments to theassay a new cut-off value of 132.10-3 was determined, which is indicatedby a dashed line.

FIG. 4 shows the PCA3/PSA performance correlated with Gleason score. In49 patients, cancer was identified by histopathological evaluation ofthe biopsies. Here the distribution of Gleason scores is shown in casesof which the PCA3/PSA test was positive/true positive and the ones inwhich the test was negative, using a cut-off value of 132×10⁻³ forPCA3/PSA ratio. Numbers of cases are on the y-axis.

FIG. 5 shows an embodiment of the present invention wherein acorrelation between Gleason scores (no malignancy and scores 4-9) andthe mean and median ratio for PCA3/PSA mRNAs in biopsies is shown.

FIG. 6 is similar to FIG. 5 except that the correlation between Gleasonscores (no malignancy and scores 4-9) and the mean and median ratio forPCA3/PSA mRNAs is presented as a graph.

FIG. 7 shows the sensitivity per grade of the method of the presentinvention using a PCA3/PSA threshold of 132×10⁻³.

FIG. 8 is similar to FIG. 7 except that the results are presented in agraph.

FIG. 9 shows the relationship between mean tumor volume and particularratios of PCA3/PSA mRNAs (i.e., below 132·10⁻³ and above 132·10⁻³).

DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

One of the major challenges for markers in prostate cancer is to meetthe need for a diagnostic test that also predicts the clinical behaviorof prostate cancer. The PCA3 gene is strongly over-expressed in prostatecancer when compared to non malignant prostate epithelial cells due to aunique mechanism of transcriptional regulation. Herein it isdemonstrated that aggressive cells are more invasive and thus are morelikely to mobilize and shed into the ductal system. In addition, it wasunexpectedly demonstrated that the PCA3/second prostate specific marker(e.g., PSA) ratio can be correlated with tumor volume. Therefore, afterextended DRE the ratio PCA3/PSA mRNA can be correlated with stage,grade, tumor volume and thus, biological aggressiveness of prostatecancer, thereby enabling a more accurate cancer diagnosis and prognosisas well as the prescription of a more appropriate treatment regime forthe patient.

Tables 4 shows the expression of PCA3 in prostate. Table 6 shows acomparison of PCA3 mRNA expression in prostate. Table 7 shows thecorrelation between PCA3/PSA and the malignancy of prostate cancer.

In one embodiment, a new cohort of patients that entered the clinic withelevated PSA serum levels (>3 ng/ml) was tested prospectively. Thepatients received study information and signed informed consent in orderto enter the study. For histological assessment, ultrasound guidedbiopsy for the presence or absence of malignancy was performed. In 49patients, cancer was identified by histopathological evaluation of thebiopsies. The histology and the PCA3/PSA mRNA ratio obtained immediatelybefore the biopsies were compared.

Surprisingly, a clear correlation was seen between Gleason score and thelevel of PCA3/PSA mRNA ratio's (FIGS. 3, 5 and 6). Subsequently, thedistribution of Gleason grades in cases of which the test waspositive/true positive and the ones in which the test was negative wasanalyzed. The false negatives were of significant lower grade than thetrue positive.

The PCA3/PSA mRNA ratio analyzed in urinary sediments after extended DREis therefore shown as a prognostic and theranostic parameter.

Despite many advances in recent years, the precision with which anindividual suffering from prostate cancer can be staged and prognosed isfar from being optimal. One of the reasons is that PSA and PSM prostatemarkers are expressed in normal and cancerous cells and that theirexpression tends to decrease in poorly differentiated tumors (which aregenerally the more aggressive type). Therefore, the diagnosis andprognosis become less and less specific and sensitive when tumors tendto be poorly differentiated (increasing tumor grade) and may even escapediagnosis.

On the other hand, PCA3 is strongly over expressed in prostate cancerwhen compared to non malignant prostate epithelial cells and theexpression of PCA3 is restricted to the prostate, due to a uniquemechanism of transcriptional regulation (Vearhaegh et al., 2000, J Biol.Chem. 275:37496-37503). It is differentially expressed in cancerous andnormal prostate cells, and its expression does not significantlydecrease with increasing tumor grade. PCA3 could therefore be a usefultool, which may overcome the drawbacks of PSA and PSM in the diagnosis,staging and treatment of prostate cancer patients.

Although PCA3 has been demonstrated to be a very specific and sensitivediagnosis tool, its value as a prognostic and theranostic tool had neverbeen established prior to the present invention. The present inventiondemonstrates that PCA3 expression correlates with biologicalaggressiveness and may therefore be used as prognostic and/ortheranostic marker. Moreover, the present invention establishes theutility of the PCA3/PSA expression level ratio as a very efficientprognostic/theranostic factor. In addition, the inventors havediscovered that the value of the PCA3/PSA expression ratio in a sampleis a very sensible and specific prognostic/theranostic tool thatcorrelates with tumor grade, tumor volume and aggressiveness of cancer.The use of PCA3 and PSA prostate markers and the fact that PSAexpression levels tend to decline with aggressiveness of prostatecancer, (which would increase the value of the ratio, a fact that isstill contested in the art) contribute to the sensibility andspecificity of the diagnostic and prognosis methods of the presentinvention.

Therefore, the present invention describes for the first time specificand sensitive methods for prognosis of prostate cancer in a patient bydetecting the level of expression (amount) of RNA encoded by the PCA3gene relatively to the level of expression of RNA encoded by the PSAgene in a sample. The value of the PCA3/PSA expression level ratio iscorrelated with the presence or absence of prostate cancer and enablesto establish the stage or aggressiveness of the disease in order todetermine cancer prognosis. This is particularly useful to determine thedegree of severity of the disease, to predict its evolution and mostimportantly to immediately choose the appropriate type of therapy forthe patient in order to increase its chances of recovery.

In general, the predisposition to develop prostate cancer, presence ofprostate cancer or aggressiveness of prostate cancer may be detected inpatients based on the presence of an elevated amount of PCA3polynucleotides in a biological sample (e.g., urine sample after DRE)relatively to the amount of PSA polynucleotides (PCA3/PSA ratio).Polynucleotides primers and probes may be used to detect the level ofmRNAs encoding PCA3 and PSA, the ratio of which is indicative of thepredisposition, presence, absence and aggressiveness (stage) of prostatecancer. In general, the elevated expression of a PCA3 marker relativelyto a PSA marker in a biological sample as compared to normal controlsamples indicates that the sample contains prostate cancer or issusceptible to develop prostate cancer. In the specific case where thesample is positive for prostate cancer, the value of the ratio betweenPCA3 and PSA expression levels correlates with a particular stage ofprogression or aggressiveness of prostate cancer (e.g., particularGleason score, tumor volume etc.).

In one embodiment, the PCA3 and PSA markers of the present invention arenucleic acids such as PCA3 and PSA mRNA or fragment thereof associatedwith prostate cancer. The PCA3 nucleic acid may have the nucleotidesequence disclosed in SEQ ID NO: 1 or 2. However, the terminology “PCA3nucleic acids” or the like is not limited to the sequences in SEQ ID NO:1 or 2, or to fragments or complements thereof. For example, PCA3nucleic acid sequences are also found under GenBank™'s accession numberAF103907. In addition, sequences which are highly homologous to suchsequences, fragments or complements thereof can also be used inaccordance with the present invention. The PSA nucleotide sequence mayhave the nucleotide sequence disclosed in SEQ ID NO 38. Of course itwill be understood that portions or fragments of PCA3 and PSA (e.g.,PCA3 and PSA nucleic acids) may be used in accordance with the presentinvention and are thus also considered as PCA3 and PSA markers.

One non-limiting example of a diagnostic and prognostic/theranosticmethod for prostate cancer comprises: (a) contacting a biological samplewith at least one oligonucleotide probe or primer that hybridizes toPCA3 nucleic acid and detecting a level of oligonucleotide thathybridizes therewith; (b) contacting the biological sample with at leastone oligonucleotide probe or primer that hybridizes with PSA nucleicacid and detecting a level of oligonucleotide that hybridizes therewith;and (c) determining the ratio between the level of oligonucleotide thathybridizes with PCA3 and the level of oligonucleotide that hybridizeswith PSA. The value of the ratio between PCA3 and PSA detected can becompared with a predetermined cut-off value and therefrom, thepredisposition, presence, absence and stage of prostate cancer as wellas the approximate tumor volume in the patient can be established.

In general, prognosis of a subject is determined to be poor (i.e. veryaggressive cancer) when the value of the PCA3/PSA mRNA ratio is superiorto 200×10⁻³. Intermediate prognosis refers to a PCA3/PSA mRNA ratiobetween 75×10⁻³ and 200×10⁻³ and good prognosis or low risk correspondsto a value of PCA3/PSA mRNA ratio between 0 and 75×10⁻³. The Gleasonscores which are associated with these ratios are >7; 6-7; and 0-5,respectively. Of course the above mentioned ranges of ratio values coulddiffer depending on the desired sensitivity and specificity of the testand on the chosen second prostate specific marker. Thus, skilled artisanwould use (and adapt) different threshold or cut-off values depending onthe particular requirements of the test.

In a particular embodiment, the polypeptide level of a second prostatespecific marker (e.g., PSA) can be used in determining a PCA3/secondprostate specific marker ratio. Thus, a diagnostic, prognostic andtheranostic method for prostate cancer may also comprise: (a) contactinga biological sample with at least one oligonucleotide probe or primerthat hybridizes to a PCA3 nucleic acid and detecting a level ofoligonucleotide that hybridizes therewith; (b) contacting the biologicalsample with at least one antibody that hybridizes with PSA polypeptideand detecting a level of polypeptide that hybridizes therewith; and (c)determining the ratio between the level of oligonucleotide thathybridizes with PCA3 and the level of antibody that hybridizes with PSApolypeptide (i.e. determining PCA3/PSA expression level ratio). Thevalue of the ratio between PCA3 and PSA detected can be compared with apredetermined cut-off value and therefrom, the predisposition, presence,absence and stage of prostate cancer as well as the approximate tumorvolume in the patient can be established. Of course, and as exemplifiedhereinbelow the PCA3/PSA ratio can be determined based on the detectionof PCA3 and PSA mRNA.

In a further embodiment, the methods of the present invention can alsobe used for monitoring the progression of prostate cancer in a patient.In this particular embodiment, the assays described above are performedover time and the variation in the ratio between the expression level ofPCA3 and PSA nucleic acids or proteins present in the sample (e.g.,urine sample) is evaluated. In general, prostate cancer is considered asprogressing when the ratio between PCA3 and PSA expression leveldetected increases with time. In contrast a cancer is not considered asprogressing when the ratio between PCA3 and PSA expression level eitherdecreases or remains constant over time.

In a related aspect, it is possible to verify the efficiency of nucleicacid amplification and/or detection only, by performing external controlreaction(s) using highly purified control target nucleic acids added tothe amplification and/or detection reaction mixture. Alternatively, theefficiency of nucleic acid recovery from cells and/or organelles, thelevel of nucleic acid amplification and/or detection inhibition (ifpresent) can be verified and estimated by adding to each test samplecontrol cells or organelles (e.g., a define number of cells from aprostate cancer cell line expressing PCA3 and second marker) bycomparison with external control reaction(s). To verify the efficiencyof both, sample preparation and amplification and/or detection, suchexternal control reaction(s) may be performed using a reference testsample or a blank sample spiked with cells, organelles and/or viralparticles carrying the control nucleic acid sequence(s). For example, asignal from the internal control (IC) sequences present into the cells,viruses and/or organelles added to each test sample that is lower thanthe signal observed with the external control reaction(s) may beexplained by incomplete lysis and/or inhibition of the amplificationand/or detection processes for a given test sample. On the other hand, asignal from the IC sequences that is similar to the signal observed withthe external control reaction(s), would confirm that the samplepreparation including cell lysis is efficient and that there is nosignificant inhibition of the amplification and/or detection processesfor a given test sample. Alternatively, verification of the efficiencyof sample preparation only may be performed using external control(s)analyzed by methods other than nucleic acid testing (e.g., analysisusing microscopy, mass spectrometry or immunological assays).

Therefore, in one particular embodiment, the methods of the presentinvention uses purified nucleic acids, prostate cells or viral particlescontaining nucleic acid sequences serving as targets for an internalcontrol (IC) in nucleic acid test assays to verify the efficiency ofcell lysis and of sample preparation as well as the performance ofnucleic acid amplification and/or detection. More broadly, the IC servesto verify any chosen step of the process of the present invention.

IC in PCR or related amplification techniques can be highly purifiedplasmid DNA either supercoiled, or linearized by digestion with arestriction endonuclease and repurified. Supercoiled IC templates areamplified much less efficiently (about 100 fold) and in a lessreproducible manner than linearized and repurified IC nucleic acidtemplates. Consequently, IC controls for amplification and detection ofthe present invention are preferably performed with linearized andrepurified IC nucleic acid templates when such types of IC are used.

The nucleic acids, cells, and/or organelles are incorporated into eachtest sample at the appropriate concentration to obtain an efficient andreproducible amplification/detection of the IC, based on testing duringthe assay optimization. The optimal number of control cells added, whichis dependent on the assay, is preferentially the minimal number of cellswhich allows a highly reproducible IC detection signal without havingany significant detrimental effect on the amplification and/or detectionof the other genetic target(s) of the nucleic acid-based assay. A sampleto which is added the purified linearized nucleic acids, cells, viralparticles or organelles is generally referred to as a “spiked sample”.

Within certain embodiments, the amount of mRNA may be detected via aRT-PCR based assay. In RT-PCR, the polymerase chain reaction (PCR) isapplied in conjunction with reverse transcription. In such an assay, atleast two oligonucleotide primers may be used to amplify a portion ofPCA3 or PSA cDNA derived from a biological sample, wherein at least oneoligonucleotide is specific for (i.e. hybridizes to) a polynucleotideencoding PCA3 or PSA RNA. The amplified cDNAs may then be separated anddetected using techniques that are well known in the art such as gelelectrophoresis and ethidium bromide staining. Amplification may beperformed on biological samples taken from a test patient and anindividual who is not afflicted with a prostate cancer (control sample),or using other types of control samples. The amplification reaction maybe performed on several dilutions of cDNA (or directly on severaldilutions of the biological sample) spanning, for example, two order ofmagnitude. A ratio value above a predetermined cut-off value isindicative of the presence, predisposition to develop prostate cancer orto a specific stage of progression (aggressiveness) of prostate cancer.In general, the elevated expression of PCA3 nucleic acid relatively tothe expression of PSA nucleic acid in a biological sample as compared tocontrol samples indicates the presence or alternatively, thepredisposition to develop lung cancer. A characteristic ratio value isalso indicative of the stage and aggressiveness of the prostate cancerdetected.

In further embodiments, PCA3 and PSA mRNAs are detected in a nucleicacid extract from a biological sample by an in vitro RNA amplificationmethod named Nucleic Acid Sequence-Based Amplification (NASBA). Numerousamplification techniques have been described and can be readily adaptedto suit particular needs of a person of ordinary skill. Non-limitingexamples of amplification techniques include strand displacementamplification (SDA), transcription-based amplification, the Qβ replicasesystem and NASBA (U.S. Pat. No. 6,124,120; Kwoh et al., 1989, Proc.Natl. Acad. Sci. USA 86, 1173-1177; Lizardi et al., 1988, BioTechnology6:1197-1202; Malek et al., 1994, Methods Mol. Biol., 28:253-260; andSambrook et al., 2000, supra). Other non-limiting examples ofamplification methods include rolling circle amplification (RCA); signalmediated amplification of RNA technology (SMART); split complexamplification reaction (SCAR); split promoter amplification of RNA(SPAR).

The amplification and/or detection of PCA3 and PSA RNA sequences can becarried out simultaneously (e.g., multiplex real-time amplificationassays.). Alternatively, oligonucleotide probes that specificallyhybridize under stringent conditions to a PCA3 or PSA nucleic acid maybe used in a nucleic acid hybridization assay (e.g., Southern andNorthern blots, dot blot, slot blot, in situ hybridization and the like)to determine the presence and/or amount of PCA3 and PSA polynucleotidein a biological sample.

Alternatively, oligonucleotides and primers could be designed todirectly sequence and assess the presence of prostate cancer specificPCA3 sequences and PSA in the patient sample following an amplificationstep. Such sequencing-based diagnostic methods are automatable and areencompassed by the present invention.

Aggressiveness of carcinomas is associated with an increase invasivepotential of the cancer cells (confirmed by down regulation of theinvasion suppressor gene E-cadherin in high grade aggressivenessprostate cancer). These invasive cells are more likely to mobilize andshed into the ductal system. The present invention takes advantages ofthe fact that the fraction of invasive cells in urinary sediment wouldincrease after extended DRE. Therefore according to the presentinvention, a preferred sample to be tested is urine obtained afterdigital rectal examination or any other methods that enable to increasethe number of prostate cells in the sample. Of course other samples suchas semen, mixed urine and semen and bladder washings may be usedaccording to the present invention, as long as the sample containssufficient material to enable the detection of PCA3 and PSA nucleicacids (or other second prostate-specific marker).

Synthesis of Nucleic Acid

The nucleic acid (e.g., DNA or RNA) for practicing the present inventionmay be obtained according to well known methods.

Isolated nucleic acid molecules of the present invention are meant toinclude those obtained by cloning as well as those chemicallysynthesized. Similarly, an oligomer which corresponds to the nucleicacid molecule, or to each of the divided fragments, can be synthesized.Such synthetic oligonucleotides can be prepared, for example, by thetriester method of Matteucci et al., J. Am. Chem. Soc. 103:3185-3191(1981) or by using an automated DNA synthesizer.

An oligonucleotide can be derived synthetically or by cloning. Ifnecessary, the 5′-ends of the oligomers can be phosphorylated using T4polynucleotide kinase. Kinasing of single strands prior to annealing orfor labeling can be achieved using an excess of the enzyme. If kinasingis for the labeling of probe, the ATP can contain high specific activityradioisotopes. Then, the DNA oligomer can be subjected to annealing andligation with T4 ligase or the like. Of course the labeling of a nucleicacid sequence can be carried out by other methods known in the art.

Primers and Probes

One skilled in the art can select the nucleic acid primers according totechniques known in the art. Samples to be tested include but should notbe limited to RNA samples from human tissue.

In one embodiment, the present invention relates to nucleic acid primersand probes which are complementary to a nucleotide sequence consistingof at least 10 consecutive nucleotides (preferably, 12, 15, 18, 20, 22,25, or 30 [of course, the sequence could be longer, see below]) from thenucleic acid molecule comprising a polynucleotide sequence at least 90%identical to a sequence selected from the group consisting of:

-   -   (a) a nucleotide sequence encoding the PCA3 mRNA comprising the        nucleotide sequence in SEQ ID NO 1 or 2;    -   (b) a nucleotide sequence encoding the PSA mRNA comprising the        nucleotide sequence in SEQ ID NO 38; and    -   (c) a nucleotide sequence complementary to any of the nucleotide        sequences in (a) or (b).

The present invention relates to a nucleic acid for the specificdetection and quantification, in a sample, of the presence of PCA3nucleic acid sequences which are associated with prostate cancer,comprising the above-described nucleic acid molecules or at least afragment thereof which binds under stringent conditions to PCA3 nucleicacid. In a related aspect, the present invention features nucleic acidfor the specific detection and quantification, in a sample, of thepresence of PSA nucleic acid sequences, comprising the above-describednucleic acid molecules or at least a fragment thereof which binds understringent conditions to PSA nucleic acids.

In one preferred embodiment, the present invention relates to oligoswhich specifically target and enable amplification (i.e. at least oneprimer for each target) of PSA and PCA3 RNA sequences associated withprostate cancer.

Oligonucleotide probes or primers of the present invention may be of anysuitable length, depending on the particular assay format and theparticular needs and targeted sequences employed. In a preferredembodiment, the oligonucleotide probes or primers are at least 10nucleotides in length (preferably, 10, 11, 12, 13, 14, 15, 16, 17, 18,19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32 . . . ) and theymay be adapted to be especially suited for a chosen nucleic acidamplification system. Longer probes and primers are also within thescope of the present invention as well known in the art. Primers havingmore than 30, more than 40, more than 50 nucleotides and probes havingmore than 100, more than 200, more than 300, more than 500 more than 800and more than 1000 nucleotides in length are also covered by the presentinvention. Of course, longer primers have the disadvantage of being moreexpensive and thus, primers having between 12 and 30 nucleotides inlength are usually designed and used in the art. As well known in theart, probes ranging from 10 to more than 2000 nucleotides in length canbe used in the methods of the present invention. As for the % ofidentity described above, non-specifically described sizes of probes andprimers (e.g., 16, 17, 31, 24, 39, 350, 450, 550, 900, 1240 nucleotides,. . . ) are also within the scope of the present invention. In oneembodiment, the oligonucleotide probes or primers of the presentinvention specifically hybridize with a PCA3 RNA (or its complementarysequence) or a PSA mRNA. More preferably, the PCA3 primers and probeswill be chosen to detect a PCA3 RNA which is associated with prostatecancer. In one embodiment, the probes and primers used in the presentinvention do not hybridize with the PCA3 or PSA genes (i.e. enable thedistinction gene and expressed PCA3 or PSA nucleic acid). Because of thestructural and sequence similarities of the PSA gene with other membersof the kallikrein gene family, the appropriate selection of PSAsequences to serve as PSA-specific probes or primers is important tomethods of amplification and/or detection of PSA specific nucleic acids.

In a further embodiment, other prostate specific markers may be used inaccordance with the present invention. Useful Examples of suitableprimers for PSA, hK2/KLK2, PSMA, amplification and detection (e.g., U.S.Pat. No. 6,551,778) are well known in the art as well as fortransglutaminase 4, acid phosphatase and PCGEM1. In one embodiment, thePSA oligonucleotide may also hybridize to other kallikrein familymembers such as kallikrein 2 (hK2/hKLK2)—One example of sucholigonucleotide is SEQ ID NO 39. Of course, PSA oligonucleotides whichare specific to PSA (i.e. designed not to hybridize to other kallikreinfamily members) can also be used. Skilled artisan can easily assess thespecificity of selected primers or probes by performing computeralignments/searches using well known databases (e.g., Genbank®).

As commonly known in the art, the oligonucleotide probes and primers canbe designed by taking into consideration the melting point ofhybridization thereof with its targeted sequence (see below and inSambrook et al., 1989, Molecular Cloning—A Laboratory Manual, 2ndEdition, CSH Laboratories; Ausubel et al., 1994, in Current Protocols inMolecular Biology, John Wiley & Sons Inc., N.Y.).

To enable hybridization to occur under the assay conditions of thepresent invention, oligonucleotide primers and probes should comprise anoligonucleotide sequence that has at least 70% (at least 71%, 72%, 73%,74%), preferably at least 75% (75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%,83%, 84%, 85%, 86%, 87%, 88%, 89%) and more preferably at least 90%(90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, 100%) identity to aportion of a PCA3 or PSA polynucleotide. Probes and primers of thepresent invention are those that hybridize to PCA3 or PSA nucleic acid(e.g., cDNA or mRNA) sequence under stringent hybridization conditionsand those that hybridize to PCA3 and PSA gene homologs under at leastmoderately stringent conditions. In certain embodiments probes andprimers of the present invention have complete sequence identity to PCA3or PSA gene sequences (e.g., cDNA or mRNA). However, probes and primersdiffering from the native PCA3 or PSA gene sequences that keep theability to hybridize to native PCA3 or PSA gene sequence under stringentconditions may also be used in the present invention. It should beunderstood that other probes and primers could be easily designed andused in the present invention based on the PCA3 and PSA nucleic acidsequence disclosed herein (SEQ ID NOs: 1, 2 and 36) by using methods ofcomputer alignment and sequence analysis known in the art (cf. MolecularCloning: A Laboratory Manual, Third Edition, edited by Cold SpringHarbor Laboratory, 2000).

For example, a primer can be designed so as to be complementary to ashort PCA3 RNA which is associated with a malignant state of theprostate cancer, whereas a long PCA3 RNA is associated with anon-malignant state (benign) thereof (PCT/CA00/01154 published under No.WO 01/23550). In accordance with the present invention, the use of sucha primer with the other necessary reagents would give rise to anamplification product only when a short PCA3 RNA) associated withprostate cancer is present in the sample. The longer PCA3 (e.g., havingan intervening sequence) would not give rise to an amplicon. Of course,the amplification could be designed so as to amplify a short (lackingall or most introns) and a long PCA3 mRNA (having at least one intron orpart thereof). In such a format, the long PCA3 mRNA could be used as thesecond prostate specific marker.

In another embodiment, primer pairs (or probes) specific for PCA3 or PSAcould be designed to avoid the detection of the PCA3 or PSA genes or ofunspliced PCA3 or PSA RNAs. For example, the primers sequences to beused in the present invention could span two contiguous exons so that itcannot hybridize to an exon/intron junction of the PCA3 or PSA genes.The amplification product obtained by the use of such primer would beintron less between two chosen exons (for examples of such primers andprobes see tables 2 to 4 below). Therefore, unspliced variants andgenomic DNA would not be amplified. It will be recognized by the personof ordinary skill that numerous probes can be designed and used inaccordance with a number of embodiments of the present invention. Suchtests can be adapted using the sequence of PCA3 and that of the secondprostate-specific marker. Of course, different primer pairs (and probes)can be designed from any part of the PCA3 sequences (SEQ ID NOs: 1, 2;see Tables 1-3 for non-limiting examples of primers and probes which canbe used to amplify or detect PCA3). Of course, primers and probes couldalso be designed based on the sequence of PSA shown in SEQ ID NO:38(GenBank® accession number M27274), as well as the sequence of othermembers of the kallikrein family, which are well-known in the art, orany other chosen second prostate specific marker (e.g., KLK2 (GenBank®acc. No. NM005551), PSMA (GenBank® acc. No. BC025672), transglutaminase4 (GenBank® acc. No. BC007003), acid phosphatase (GenBank® acc. No.BC016344), PCGEM 1 (GenBank® acc. No. AF223389).

Probes of the invention can be utilized with naturally occurring sugarphosphate backbones as well as modified backbones includingphosphorothioates, dithionates, alkyl phosphonates and a nucleotides andthe like. Modified sugar phosphate backbones are generally taught byMiller, 1988, Ann. Reports Med. Chem. 23:295 and Moran et al., 1987,Nucleic Acids Res., 14:5019. Probes of the invention can be constructedof either ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), andpreferably of DNA.

Although the present invention is not specifically dependent on the useof a label for the detection of a particular nucleic acid sequence, sucha label might be beneficial, by increasing the sensitivity of thedetection. Furthermore, it enables automation. Probes can be labeledaccording to numerous well-known methods (Sambrook et al., 2000, supra).Non-limiting examples of detectable markers and labels include ³H, ¹⁴C,³P, and ³S, ligands, fluorophores, chemiluminescent agents, enzymes, andantibodies. Other detectable markers for use with probes, which canenable an increase in sensitivity of the method of the invention,include biotin and radionucleotides. It will become evident to theperson of ordinary skill that the choice of a particular label dictatesthe manner in which it is bound to the probe.

As commonly known, radioactive nucleotides can be incorporated intoprobes of the invention by several methods. Non-limiting examplesthereof include kinasing the 5′ ends of the probes using gamma ³²P ATPand polynucleotide kinase, using the Klenow fragment of Pol I of E. coliin the presence of radioactive dNTP (e.g., uniformly labeled DNA probeusing random oligonucleotide primers), using the SP6/T7 system totranscribe a DNA segment in the presence of one or more radioactive NTP,and the like.

In one embodiment, the label used in a homogenous detection assay is achemiluminescent compound (e.g., U.S. Pat. Nos. 5,656,207; 5,658,737 and5,639,604), more preferably an acridinium ester (“AE”) compound, such asstandard AE or derivatives thereof. Methods of attaching labels tonucleic acids and detecting labels are well known (e.g., see Sambrook etal., Molecular Cloning, A Laboratory Manual, 2nd ed. (Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y., 1989), Chapt. 10; U.S. Pat.Nos. 5,658,737, 5,656,207, 5,547,842; 5,283,174 and 4,581,333; andEuropean Pat. App. No. 0 747 706). Preferred methods of labeling a probewith an AE compound attached via a linker have been previously describedin detail (e.g., see U.S. Pat. No. 5,639,604, see in Example 8,thereof).

Amplification of a selected, or target, nucleic acid sequence may becarried out by a number of suitable methods. See generally Kwoh et al.,1990, Am. Biotechnol. Lab. 8:14 25. Numerous amplification techniqueshave been described and can be readily adapted to suit particular needsof a person of ordinary skill. Non-limiting examples of amplificationtechniques include polymerase chain reaction (PCR, RT PCR, real-timeRT-PCR, etc.), ligase chain reaction (LCR), strand displacementamplification (SDA), transcription based amplification, the Qβ replicasesystem and NASBA (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA 86:1173-1177; Lizardi et al., 1988, BioTechnology 6:1197-1202; Malek etal., 1994, Methods Mol. Biol., 28:253 260; and Sambrook et al., 2000,supra). Other non-limiting examples of amplification methods have beenlisted above.

Non-limiting examples of suitable methods to detect the presence of theamplified products include the followings: agarose or polyacrylamidegel, addition of DNA labelling dye in the amplification reaction (suchas ethidium bromide, Picogreen™, SYBER green, etc.) and detection withsuitable apparatus (fluorometer in most cases). Other suitable methodsinclude sequencing reaction (either manual or automated); restrictionanalysis (provided restriction sites were built into the amplifiedsequences), or any method involving hybridization with a sequencespecific probe (Southern or Northern blot, TaqMan probes, molecularbeacons, and the like). Of course, other amplification methods areencompassed by the present invention. Molecular beacons are exemplifiedherein as one method for detecting the amplified products according tothe present invention (see below).

Of course in some embodiment direct detection (e.g., sequencing) of PCA3cancer specific sequences as well as that of another prostate specificmarker (e.g., PSA) in a sample may be performed using specific probes orprimers.

In one embodiment, the present invention has taken advantage oftechnological advances in methods for detecting and identifying nucleicacids. Therefore, the present invention is suitable for detection by oneof these tools called molecular beacons.

Molecular beacons are single-stranded oligonucleotide hybridizationprobes/primers that form a stem loop structure. The loop contains aprobe sequence that is complementary to a target sequence, and the stemis formed by the annealing of complementary arm sequences that arelocated on either side of the probe/primer sequence. A fluorophore iscovalently linked to the end of one arm and a quencher is covalentlylinked to the end of the other arm. Molecular beacons do not fluorescewhen they are free in solution. However, when they hybridize to anucleic acid strand containing a target sequence they undergoconformational change that enables them to fluoresce brightly (see U.S.Pat. Nos. 5,925,517, and 6,037,130). Molecular beacons can be used asamplicon detector probes/primers in diagnostic assays. Becausenonhybridized molecular beacons are dark, it is not necessary to isolatethe probe-target hybrids to determine for example, the number ofamplicons synthesized during an assay. Therefore, molecular beaconssimplify the manipulations that are often required when traditionaldetection and identifications means are used.

By using different colored fluorophores, molecular beacons can also beused in multiplex amplification assays such as assays that target thesimultaneous amplification and detection of PCA3 nucleic acid and of thesecond specific prostate nucleic acid (e.g., PSA, [GenBank® acc. No.M27274, SEQ ID NO 38] hK2/KLK2 [GenBank® acc. No. NM005551], PSMA[GenBank® acc. No. BC025672], transglutaminase 4 [GenBank® acc. No.BC007003], acid phosphatase [GenBank® acc. No. BC016344], and PCGEM1[GenBank® acc. No. AF223389]). The design of molecular beaconsprobes/primers is well known in the art and softwares dedicated to helptheir design are commercially available (e.g., Beacon designer fromPremier Biosoft International). Molecular beacon probes/primers can beused in a variety of hybridization and amplification assays (e.g., NASBAand PCR).

In accordance with one embodiment of the present invention, theamplified product can either be directly detected using molecularbeacons as primers for the amplification assay (e.g., real-timemultiplex NASBA or PCR assays) or indirectly using, internal to theprimer pair binding sites, a molecular beacon probe of 18 to 25nucleotides long (e.g., 18, 19, 20, 21, 22, 23, 24, 25) whichspecifically hybridizes to the amplification product. Molecular beaconsprobes or primers having a length comprised between 18 and 25nucleotides are preferred when used according to the present invention(Tyagi et al., 1996, Nature Biotechnol. 14: 303-308). Shorter fragmentscould result in a less fluorescent signal, whereas longer fragmentsoften do not increase significantly the signal. Of course shorter orlonger probes and primers could nevertheless be used.

Examples of nucleic acid primers which can be derived from PCA3 RNAsequences are shown hereinbelow in Tables 2-4.

Examples of nucleic acid primers which can be derived from PSA (e.g.,SEQ ID NO 11), RNA sequences are shown hereinbelow. Other primers of thepresent invention can be derived from PSA. Of course other variants wellknown in the art can also be used (U.S. Pat. Nos. 6,479,263 and5,674,682) as second prostate specific marker. Because of the structuraland sequence similarities of the PSA gene with other members of thekallikrein gene family, the appropriate selection of PSA sequences toserve as PSA-specific probes or primers is important to methods ofamplification and/or detection of PSA specific nucleic acids. Examplesof suitable primers for PSA, hK2/KLK2, PSMA, amplification and detection(e.g., U.S. Pat. No. 6,551,778) are well known in the art as well as fortransglutaminase 4, acid phosphatase and PCGEM1. In one embodiment, thePSA oligonucleotide may also hybridize to other kallikrein familymembers such as kallikrein 2 (hK2/hKLK2). One example of such anoligonucleotide is SEQ ID NO 12.

It should be understood that the sequences and sizes of the primerstaught in Tables 2-4 are arbitrary and that a multitude of othersequences can be designed and used in accordance with the presentinvention.

While the present invention can be carried out without the use of aprobe which targets PCA3 sequences, such as the exon junctions of PCA3in accordance with the present invention, such probes can add a furtherspecificity to the methods and kits of the present invention.Non-limiting examples of specific nucleic acid probes which can be usedin the present invention (and designed based on the exonic sequencesshown in Table 2) are set forth in Table 3, below.

Generally, one primer in the amplification reaction hybridizesspecifically to a sequence in a first exon (or upstream exon) and theother primer used in the amplification reaction hybridizes specificallyto a sequence in a second exon (or downstream exon), and the probehybridizes to a sequence that spans the 3′ region of the first exon andthe 5′ region of the second exon. That is, the probe is specific for achosen exon-exon junction in an amplified sequence made from a splicedPCA3 RNA that lacks at least one intron between the upstream anddownstream exon sequences to which the primers hybridize. Primers foruse in amplifying sequences of the spliced RNA that contain a chosenexon-exon junction can readily be determined by using standard methods,so long as the region amplified by the primer pair contains theexon-exon junction sequence or its complementary sequence. Any method ofnucleic acid amplification may be used to amplify the sequence thatcontains the chosen exon-exon junction and procedures for using any of avariety of well-known amplification methods can readily be determined bythose skilled in the art.

Probes that detect a chosen exon-exon junction may be labeled with anyof a variety of labels that can, directly or indirectly, result in asignal when the probe is hybridized to the amplified sequence thatcontains the exon-exon junction. For example, a label may be any moietythat produces a colorimetric, luminescent, fluorescent, radioactive, orenzymatic signal that can be detected by using methods well known in theart. A probe need not be labeled with a label moiety if binding of theprobe specifically to the amplified nucleic acid containing theexon-exon junction results in a detectable signal, such as, for examplea detectable electrical impulse.

Examples of amplification primer pair combinations that amplify nucleicacid sequence that includes an exon-exon junction and embodiments ofsome exon-exon junction probe sequences are shown in Table 4. It will beunderstood by those skilled in the art that the probe sequences shownbelow also include the complementary sequences of the sequences shown,and sequences that include insignificant changes to the specificsequences shown (i.e., the changes do not affect the ability of a probeto hybridize specifically to the chosen exon-exon junction sequence,under standard hybridization conditions). Furthermore, although theprobe sequences are shown as DNA sequences, those skilled in the artwill understand that the corresponding RNA sequences or theircomplementary sequences may be used as probes. Also, the backbonelinkages of the probe base sequences may include one or more standardRNA linkages, DNA linkages, mixed RNA-DNA linkages, or other linkagessuch as 2′-O-methyl linkages or peptide nucleic acid linkages, all ofwhich are well known to those skilled in the art.

As shown in Table 4 (first column), the chosen exon-exon junction to bedetected may join exons 1 and 2 (exon 1/exon 2), exons 1 and 3 (exon1/exon 3), exons 2 and 3 (exon 2/exon 3), or exons 3 and 4 (exon 3/exon4). Primer pairs are sequences located in two different exons thatdirectly or indirectly flank the chosen exon-exon junction (Table 4,second column). Thus, for an exon 1/exon 2 junction, the primer pairsare one primer specific for a sequence contained in exon 1 and anotherprimer specific for a sequence contained in exon 2. But for detecting anexon 2/exon 3 junction or an exon 3/exon 4 junction, the primer pairsmay be selected from more than two different exons (see below in column2) so long as the amplified sequence contains the chosen exon-exonjunction region. The “exon 4” primers include primers specific for asequence contained in any sequence of exons 4a, 4b, 4c, or 4d.

Of course, as will be understood by the person of ordinary skill, amultitude of additional probes can be designed from the same or otherregion of SEQ ID NO. 1 as well as from SEQ ID NO. 2 and 38 and othersequences of the present invention, whether they target exon junctionsor not. It will be clear that the sizes of the probes taught in Tables 2and 3 are arbitrary and that a multitude of other sequences can bedesigned and used in accordance with the present invention.

It will be readily recognized by the person of ordinary skill, that thenucleic acid sequences of the present invention (e.g., probes andprimers) can be incorporated into anyone of numerous established kitformats which are well known in the art.

In one embodiment of the above-described method, a nucleic acid probe isimmobilized on a solid support. Examples of such solid supports include,but are not limited to, plastics such as polycarbonate, complexcarbohydrates such as agarose and sepharose, and acrylic resins, such aspolyacrylamide and latex beads. Techniques for coupling nucleic acidprobes to such solid supports are well known in the art.

The test samples suitable for nucleic acid probing methods of thepresent invention include, for example, cells or nucleic acid extractsof cells, or biological fluids (e.g., urine). The sample used in theabove-described methods will vary based on the assay format, thedetection method and the nature of the tissues, cells or extracts to beassayed. Methods for preparing nucleic acid extracts of cells are wellknown in the art and can be readily adapted in order to obtain a samplewhich is compatible with the method utilized. Preferably the sample is aurine sample. When the urine sample is used, it should contain at leastone prostate cell in order to enable the identification of the prostatespecific markers (e.g., PCA3 and PSA) of the present invention. In fact,assuming that the half-life of PCA3 mRNA in an untreated biologicalsample is not suitable for easily enabling the preservation of theintegrity of its sequence, the collected sample, whether urine orotherwise, should, prior to a treatment thereof contain at least oneprostate cell. It will be recognized that the number of cells in thesample will have an impact on the validation of the test and on therelative level of measured PCA3 (or PSA or other prostate specificmarker).

Kits for the Detection of PCA3 and PSA mRNA

In another embodiment, the present invention relates to a kit fordiagnosing prostate cancer in a manner which is both sensitive andspecific (i.e., lowering the number of false positives). Such kitgenerally comprises a first container means having disposed therein atleast one oligonucleotide probe or primer that hybridizes to a prostatecancer-specific PCA3 nucleic acid sequence. In one embodiment, thepresent invention also relates to a kit further comprising in a secondcontainer means oligonucleotide probes or primers which are specific toa further prostate specific marker (e.g., PSA), thereby enabling thedetermination of a ratio as well as validating a negative result withPCA3. In another embodiment, the present invention relates to a kitfurther comprising in a second container means, antibodies which arespecific to a further prostate specific marker, thereby validating thepresence of prostate cells in a sample.

In a particular embodiment of the present invention, this kit comprisesa primer pair which enables the amplification of PCA3 and at least oneprostate specific marker selected from PSA, hK2/KLK2, PSMA,transglutaminase 4, acid phosphatase and PCGEM1. In a preferredembodiment the prostate specific marker is PSA nucleic acid or PSAprotein. Of course the present invention also encompasses the use of athird prostate specific marker.

Oligonucleotides (probes or primers) of the kit may be used, forexample, within a NASBA, PCR or hybridization assay. Amplificationassays may be adapted for real time detection of multiple amplificationproducts (i.e., multiplex real time amplification assays).

In a related particular embodiment, the kit further includes othercontainers comprising additional components such as additionaloligonucleotide or primer and/or one or more of the following: buffers,reagents to be used in the assay (e.g., wash reagents, polymerases orinternal control nucleic acid or cells or else) and reagents capable ofdetecting the presence of bound nucleic acid probe or primers. Examplesof detection reagents include, but are not limited to radiolabelledprobes, enzymatic labeled probes (horse radish peroxidase, alkalinephosphatase), and affinity labeled probes (biotin, avidin, orsteptavidin). Of course the separation or assembly of reagents in sameor different container means is dictated by the types of extraction,amplification or hybridization methods, and detection methods used aswell as other parameters including stability, need for preservation etc.It will be understood that different permutations of containers andreagents of the above and foregoing are also covered by the presentinvention. The kit may also include instructions regarding eachparticular possible diagnosis, prognosis, theranosis or use, bycorrelating a corresponding ratio of PCA3 mRNA level over PSA mRNA levelwith a particular diagnosis, prognosis, theranosis or use, as well asinformation on the experimental protocol to be used.

In one embodiment, the detection reagents are molecular beacon probeswhich specifically hybridizes to the amplification products. In anotherembodiment, the detection reagents are chemiluminescent compounds suchas Acridinium Ester (AE).

For example, a compartmentalized kit in accordance with the presentinvention includes any kit in which reagents are contained in separatecontainers. Such containers include small glass containers, plasticcontainers or strips of plastic or paper. Such containers allow theefficient transfer of reagents from one compartment to anothercompartment such that the samples and reagents are not crosscontaminated and the agents or solutions of each container can be addedin a quantitative fashion from one compartment to another. Suchcontainers will include a container which will accept the test sample(e.g., an RNA extract from a biological sample or cells), a containerwhich contains the primers used in the assay, containers which containenzymes, containers which contain wash reagents, and containers whichcontain the reagents used to detect the extension products. As mentionedabove, the separation or combination of reagents can be adapted by theperson of ordinary skill to which this invention pertain, according tothe type of kit which is preferred (e.g., a diagnostic kit based onamplification or hybridization methods or both), the types of reagentsused and their stability or other intrinsic properties. In oneembodiment, one container contains the amplification reagents and aseparate container contains the detection reagent. In anotherembodiment, amplification and detection reagents are contained in thesame container.

Kits may also contain oligonucleotides that serve as capture oligomersfor purifying the target nucleic acids from a sample. Examples ofcapture oligomers have sequences of at least 15 nucleotidescomplementary to a portion of the PCA3 target nucleic acid. Embodimentsof capture oligomers may have additional bases attached to a 3′ or 5′end the sequence that is complementary to the PCA3 target sequence whichmay act functionally in a hybridization step for capturing the targetnucleic acid. Such additional sequences are preferably a homopolymerictail sequence, such as a poly-A or poly-T sequence, although otherembodiments of tail sequences are included in capture oligomers of thepresent invention. In one embodiment, CAP binding protein (e.g.,elF4G-4E) or part thereof may be used to capture cap-structurecontaining mRNAs (Edery et al., 1987, Gene 74(2): 517-525). In anotherembodiment, a non specific capture reagent is used (e.g., silica beads).

Kits useful for practicing the methods of the present invention mayinclude those that include any of the amplification oligonudeotidesand/or detection probes disclosed herein which are packaged incombination with each other. Kits may also include capture oligomers forpurifying the PCA3 target nucleic acid from a sample, which captureoligomers may be packaged in combination with the amplificationoligonucleotides and/or detection probes. Finally, the kits may furtherinclude instructions for practicing the diagnostic, theranostic and/orprognostic methods of the present invention. Such instructions canconcern details relating to the experimental protocol as well as to thecut-off values that may be used.

In a further embodiment, cells contained in voided urine samplesobtained after an attentive digital rectal examination are harvested andlysed in a lysis buffer. Nucleic acids are extracted (e.g., from thelysate by solid phase extraction on silica beads for example). Detectionof the presence of RNA encoded by the PCA3 gene in the nucleic acidextract is done by an in vitro specific RNA amplification coupled toreal-time detection of amplified products by fluorescent specificprobes. In this method, simultaneously to the amplification of the PCA3prostate cancer specific RNA undergoes the amplification of the secondprostate-specific marker (such as the PSA RNA) as a control for thepresence in the urine sample of prostate cells.

The screening and diagnostic methods of the invention do not requirethat the entire PCA3 RNA sequence be detected. Rather, it is onlynecessary to detect a fragment or length of nucleic acid that issufficient to detect the presence of the PCA3 nucleic acid from a normalor affected individual, the absence of such nucleic acid, or an alteredstructure of such nucleic acid (such as an aberrant splicing pattern).For this purpose, any of the probes or primers as described above isused, and many more can be designed as conventionally known in the artbased on the sequences described herein and others known in the art.

It is to be understood that although the following discussion isspecifically directed to human patients, the teachings are alsoapplicable to any animal that expresses PCA3.

The method of the present invention may also be used to monitor theprogression of prostate cancer in patient as described above.

The present invention is illustrated in further details by the followingnon-limiting example. The examples are provided for illustration onlyand should not be construed as limiting the scope of the invention.

Example 1 The PCA3/PSA mRNA Ratios Correlate with Histological Grade inthe Biopsy

In order to determine if the expression level ratio between PCA and PSAwould be a good prognostic and theranostic tool, a study on ˜150patients presenting elevated serum PSA levels (>3 ng/ml), as anindication for ultrasound guided biopsy and histological assessment ofpresence/absence of malignancy was conducted. Patients received studyinformation and informed consent was required to enter into the study.Cancer was identified and confirmed in 49 patients by guided biopsy andhistological grade analysis. The number of events, with histology in theGS area now considered to be the most difficult to assess biologicalaggressiveness in (38 cases with a biopsy GS of 6 and 7).

In urinary sediments, following extended DRE, the ratio PCA3/PSA mRNAwas evaluated in view of assessing whether this ratio could becorrelated with biological aggressiveness. PSA mRNA levels were used tonormalize the test, to correct for total number of prostate born cellsin the specimen.

In FIG. 3, the PCA3/PSA mRNA ratio is confronted with the histologicalgrade. There is a clear correlation with Gleason score and the level ofPCA3/PSA mRNA ratios between GS 5-8. The mean value of the PCA3/PSAratio in case of Gleason IV and V is 41, in case of Gleason VI it is163, in case of Gleason VII it is 193 and in case of Gleason VIII it is577 (FIG. 3). Note, that in the three GS 9 cases there seems to be adecrease.

The ‘distribution’ of Gleason Grades in cases in which the test waspositive (‘true positive’) and in the ones in which the test wasnegative (‘false negative’) was then analyzed (FIG. 4). The resultsdemonstrate that the PCA3/PSA mRNA ratio test using urinary sedimentsafter extended DRE is significantly more positive in the high gradecancers. This study corroborates the hypothesis that PCA3/PSA mRNAratios can serve as a prognostic factor.

Example 2 PCA3 Gene Based Analysis of Urinary Sediments has PrognosticValue

A new cohort of approximately 300 patients with elevated serum levels(>3 ng/ml) was tested as in Example 1. The patients received studyinformation and signed informed consent in order to enter the study. Forhistological assessment ultrasound guided biopsy for the presence orabsence of malignancy was performed. In 108 patients cancer wasidentified by histopathological evaluation of the biopsies. We comparedthe histology with the PCA3/PSA mRNA ratio obtained immediately beforethe biopsies.

As seen in FIGS. 5-6, a clear correlation was seen between Gleason (sum)score and the level of PCA3/PSA mRNA ratios. Subsequently, thedistribution of Gleason grades, in cases of which the test waspositive/true positive and the ones in which the test was negative, wasanalyzed. The sensitivity per grade is given using a threshold of132.10-3. The sensitivity to detect high grade (aggressive) cancers ishigher. In other words, the false negatives were of significant lowergrade than the true positive (FIGS. 7 and 8).

In view of the above it can be concluded that the PCA3/PSA mRNA ratio,analyzed in urinary sediments after extended DRE, constitutes a strongtheranostic, diagnostic and prognostic tool.

Example 3 Detailed Analysis of Histopathological Parameters and PCA3Test Results

PCA3 gene expression is prostate-specific and is strongly up-regulatedin prostate cancer cells compared to non-malignant prostate cells. Itwas successfully demonstrated that PCA3 gene-based analysis can detectprostate cancer cells in urinary sediments after extended DRE 1 and 2above. Consequently PCA3 has been shown to have tremendous potential inprostate cancer diagnosis. Having now demonstrated that more aggressivetumors could grow in a more invasive manner and shed more cancer cellsin the prostatic ducts, it was also demonstrated that PCA3 gene-basedanalysis correlates with increasing Gleason score in biopsies andtherefore has potential as a prognostic parameter (see Examples 1 and 2above). In this subgroup analysis, the histopathological parameters ofthe radical prostatectomy specimens were correlated to the results ofPCA3 gene-based analysis.

In the clinic, a cohort of prostate cancer patients received informationand signed informed consent in order to enter the study. 48 of thesepatients were treated by radical prostatectomy. The histopathologicalparameters of the radical prostatectomy specimens were compared to theratio of PCA3/PSA mRNA in urinary sediments obtained before the surgery.All prognostic parameters were compared.

As seen in FIG. 9, a correlation between the total tumor volume in theradical prostatectomy specimens and the level of the ratio PCA3/PSA mRNAwas observed.

Thus, the PCA3/PSA mRNA ratio has prognostic value with respect to thetotal tumor volume in prostate cancer patients and therefore to thestage/grade and aggressiveness of prostate cancer. By using the PCA3/PSAmRNA ratio, it is thus possible not only to determine tumor grade, butalso to evaluate tumor size. As a result of the PCA3/PSA mRNA ratioanalysis, an appropriate treatment regimen adapted for each patient canbe established. In addition, the use of the PCA3/PSA mRNA ratio allowsto more accurately prognose the outcome of the disease.

Example 4 Quantitative RT-PCR Assay for PCA3 and PSA mRNAS Materials andMethods Tissue Specimens

Radical prostatectomy specimens were obtained from the CanisiusWilhelmina Hospital Nijmegen and the University Medical Center Nijmegen.Normal prostate, BPH and prostate tumor specimens were freshly obtained,snap frozen in liquid nitrogen and processed by step sectioning. Atregular intervals a Hematoxilin & Eosin staining was performed todetermine the percentage of normal, BPH and tumor cells in the tissuesections. Gleason scores and TNM classification of these tumors weredetermined at the department of Pathology of both hospitals. Total RNAwas extracted from these tissue specimens using the LiCl-urea method(22).

Production of PCA3 and IS-PCA3 RNA

The internal standard (IS-PCA3) was constructed using the “GeneEditor”in vitro site-directed mutagenesis system (Promega). Three substitutions(TCC to CGT) at positions 416 to 418 of the PCA3 cDNA (GenBank™#AF103907) were introduced in the PCA3 cDNA construct (pMB45). Mutationswere confirmed by DNA sequence analysis.

Linearized pMB45 and pMB45-mutant plasmid DNA served as a template forin vitro transcription reactions using T3 RNA polymerase (RocheDiagnostics). In vitro produced RNAs were DNase-I treated, purified byphenol extraction, precipitated and dissolved indiethylpyrocarbonate-treated water. The concentration and integrity ofthe RNAs were determined by agarose gel electrophoresis using RNAstandards. The RNAs were stored in aliquots at −70° C.

Reverse Transcriptase Reaction

In vitro produced PCA3 RNA and IS-PCA3 RNA as well as tissue RNA wereused as templates for cDNA synthesis using the first-strand cDNAsynthesis Kit (Amersham Biosciences). PCA3 and IS-PCA3 RNAs were dilutedin 0.2 mg/ml E. coli tRNA (Roche Diagnostics) which was used as acarrier RNA solution. For the preparation of an extended calibrationcurve, 5·10³ copies of IS-PCA3 RNA were mixed with a variable amount (50to 1·10⁷ copies) of PCA3 RNA. For the determination of PCA3 in a tissuesample, total RNA was mixed with 5·10³ copies of IS-PCA3 RNA. The RNAmixtures were heated for 10 minutes at 65° C., followed by quenching onice. To the RNA, 0.2 g of universal oligo-d(T)₁₈ primer, 2 mM DTT and 5μl of a Bulk 1^(st) strand reaction mixture (Amersham Biosciences) wereadded, in a final reaction volume of 15 μl. The samples were incubatedfor 1 hour at 37° C. and the obtained cDNA samples were heated for 5minutes at 95° C.

PCR amplification

For PCR amplifications, the following PCA3-specific primers were used:forward 5′-TGGGAAGGACCTGATGATACA-3′ (SEQ ID NO: 40 nucleotides 97-108 ofexon 1 of the PCA3 cDNA, GenBank™ #AF103907) and reverse5′-CCCAGGGATCTCTGTGCTT-3′ (SEQ ID NO: 41 nucleotides 459-477, spanningexons 3 and 4 of the PCA3 cDNA). The reverse primer was biotinylated.Five microliters of cDNA sample was amplified in a 100 μl PCR reactioncontaining: 0.133 μM reverse primer, 0.065 μM biotinylated reverseprimer, 0.2 μM forward primer, 250 mM deoxynucleotide triphosphates(Roche Diagnostics), 2 Units of Super Taq™ polymerase (HT BiotechnologyLTD) in buffer containing 1.5 mM magnesium chloride, 10 mM Tris-HCl (pH8.3), 50 mM potassium chloride and 0.1% Triton X-100. The reactionmixtures were overlaid with mineral oil and thermocycling was performedon a Thermal Cycler™ (PerkinElmer Lifesciences Inc.) as follows: 95° C.for 2 minutes followed by 35 cycles of 95° C. for 1 minute, 60° C. for 1minute, 72° C. for 1 minute; followed by a final extension of 72° C. for10 minutes.

Hybridization Assay

The PCR products obtained were purified from mineral oil. Tenmicroliters of each PCR product were added to a well of astreptavadin-coated microtitration plate (InnoTrac Diagnostics) intriplicate. Fifty microliters of DELFIA® Assay buffer containing 1.5 MNaCl was added to each well. The biotinylated PCR products were capturedto the streptavadin-coated well for 1 hour at room temperature underslow shaking. The samples were washed three times with DELFIA® washsolution. The double-stranded PCR products were denatured using 100 μl50 mM NaOH solution, for 5 minutes at room temperature under slowshaking. The samples were washed three times with DELFIA® wash solutionto remove the denatured, non-bound, DNA strands. PCA3 detection probe(30 pg/μl) labeled with Eu³⁺ (SEQ ID NO: 425′(modC)₂₀CACATTTCCAGCCCCT-3′) and IS-PCA3 detection probe (30 pg/μl)labeled with Tb³⁺ (SEQ ID NO: 435′(modC)₂₀CACATTCGTAGCCCCT-3′) wereadded to each well in DELFIA® Assay Buffer containing 1.5 M NaCl and 5g/L non-fat milk powder. The detection probes were hybridized to thecaptured PCA3 and IS-PCA3 DNA strands for 2.5 hours at 37° C. Thesamples were washed six times with DELFIA® wash solution at roomtemperature. Then 200 μl of DELFIA® Enhancement solution was added toeach well. Free Eu³′ rapidly forms a highly fluorescent and stablechelate with the components of the DELFIA®(Eu³⁺) Enhancement Solution.After incubation for 30 minutes at room temperature under slow shaking,the fluorescent signal obtained from the Eu³ chelates was measured witha 1420 Victor™ Multilabel Counter. Then 50 μl of DELFIA® (Tb³⁺) EnhancerSolution was added to each well to form a highly fluorescent chelatewith Tb³⁺. After incubation for 5 minutes at room temperature under slowshaking, the fluorescent signal obtained from the Tb³ chelates wasmeasured. All the DELFIA® reagents and the 1420 Victor™ MultilabelCounter were obtained from PerkinElmer Life Sciences.

Statistical Analysis

Using the Statistical Package for Social Sciences (SPSS) the data weresummarized in a Receiver Operating Characteristic Curve (ROC) tovisualize the efficacy of PCA3 as a marker. In this curve thesensitivity (true positives) was plotted on the Y-axis against1-specificity (false positives) on the X-axis. In this curve allobserved values were considered as arbitrary cut-off values. The AreaUnder Curve (AUC) and its 95% confidence interval (CI) were calculatedas a measure for the discriminative efficacy of the tested marker. Ifthe marker has no discriminative value, the AUC value is close to 0.5.In this case the AUC will be close to the diagonal in the curve. If amarker has strong discriminative power, the ROC curve will be close tothe upper left corner (AUC is close to 1).

FIGS. 2A and B show that the PCA3/PSA ratio is a powerful and validatedmarker for prostate cancer diagnosis.

Example 5 Time-Resolved Fluorescence-Based Quantitative Determination ofPCA3 mRNA: a Sensitive Tool for Prostate Cancer Prognosis

For materials and methods see Example 4.

Optimization of the Hybridization Assay

Biotinylated PCR products of either PCA3 or IS-PCA3 were used foroptimizing the reaction conditions of the hybridization assay. For bothtargets and their hybridization probes best fluorescent signals withhigh signal to background ratios were obtained after 150 minutes ofincubation at 37° C. in the presence of 1.5 M NaCl and 5 g/L non-fatmilk powder. Sodium chloride was used to enhance the hybridization andthe function of non-fat milk powder was to block non-specific backgroundsignal. Under these stringent conditions, best efficiency of thehybridization assay was obtained using 30 pg/μl of each probe.

To verify the possibility of cross-hybridization between targets andprobes, 1·10² to 1·10⁷ molecules of either PCA3 or IS-PCA3 RNA were usedas templates in RT-PCR. The biotinylated PCR products were thenhybridized to both probes. Only after amplification of 1·10⁶ IS-PCA3 RNAmolecules, the PCA3 probe showed slight cross-reactivity (0.1%) with theIS-PCA3 target. Under these optimized conditions, the IS-PCA3 probeshowed no detectable cross-reactivity with the PCA3 target. The slightcross-reactivity of the PCA3 probe is due to the stability of themismatches. The binding of the PCA3 probe to the IS-PCA3 target is morestable than the binding of the IS-PCA3 probe to the PCA3 target.

PCR Amplification

The best efficiency of PCR amplification was obtained using 0.2 μM ofeach primer. Ylikoski (1999) showed that large excess of biotinylatedreverse primer competed with the biotinylated PCR product forstreptavidin binding-sites (23). Therefore, a reduced amount ofbiotinylated reverse primer was used to avoid a dilution step ofamplification products before the hybridization assay and to obtain areliable detection of the amplification products. For optimal PCRamplification 0.133 M unlabeled reverse primer, 0.065 M biotinylatedreverse primer, and 0.2 M forward primer were used.

To determine the amplification efficiency of both PCA3 and IS-PCA3targets, 5·10³ molecules of either PCA3 RNA or IS-PCA3 RNA wereamplified by RT-PCR for different numbers of amplification cycles.Raeymaekers (1993) showed that the PCR efficiency was based on theequation for exponential growth: log Nc=log Ni+c[log(1+f)] in which Ncis the amount of product generated after c amplification cycles, Ni isthe initial amount of target, c is the number of amplification cyclesand f is the amplification efficiency (24). When log Nc is plottedagainst the number of amplification cycles, then the slope of the curveequals log(1+f). If the amplification efficiency is the same for bothPCA3 and IS-PCA3 targets then the slope of both curves is the same. BothPCA3 (f=0.63) and IS-PCA3 (f=0.64) were reverse transcribed andamplified with identical efficiencies (data not shown). This wasconfirmed when the log of the PCA3/IS-PCA3 ratio was plotted against thenumber of amplification cycles. A horizontal line was generatedindicating that the amplification efficiency is the same for bothtargets (data not shown).

The sensitivity and the analytical range of the PCA3-based assay may beaffected by the amount of IS-PCA3 RNA that is added to each sample. Forexample, if the amount of internal standard amplified with varyingamounts of PCA3 is too high, small amounts of PCA3 RNA cannot beamplified sufficiently by RT-PCR to generate a detectable signal.Consequently, the sensitivity of the technique becomes limited. The sameholds true for the RT-PCR amplification of a too small amount of IS-PCA3RNA in the presence of a high concentration of PCA3 RNA. Therefore, theinterference between amplification of the PCA3 and IS-PCA3 targets wasstudied by RT-PCR amplification of varying amounts of PCA3 RNA with aconstant amount of IS-PCA3 RNA. The fluorescent signals obtained for5·10³ or 5·10⁴ IS-PCA3 molecules remained constant afterco-amplification with 1·10² to 5·10⁵ PCA3 molecules. Only after theco-amplification with more than 1·10⁸ PCA3 molecules, did thefluorescent signals for both IS-PCA3 and PCA3 slightly decrease (datanot shown). This phenomenon is due to competition of both targetmolecules during PCR as well as to the saturation phase of the PCRreaction. These data indicate that both concentrations of IS-PCA3 can beused for co-amplification of PCA3 to obtain a wide linear range for thequantification of PCA3. When variable amounts of IS-PCA3 wereco-amplified with a constant amount of PCA3, similar results wereobtained (data not shown).

Detection Limit and Reproducibility

To determine the sensitivity and linearity of the proposed quantitativeRT-PCR technique for the detection and quantification of PCA3 RNA, acalibration curve was generated. Varying amounts of PCA3 RNA molecules(ranging from 50 to 1·10⁷ PCA3 RNA molecules) were mixed with 5·10³IS-PCA3 RNA copies. As was shown before, this was the smallest amount ofIS-PCA3 that allowed a wide linear range for quantification of PCA3.Furthermore, the slight cross-reactivity (0.1%) of the PCA3 probe withmore than 5·10⁵ IS-PCA3 copies could be avoided using this amount ofIS-PCA3. The background signal was defined as the signal obtained whenno PCA3 RNA or IS-PCA3 RNA was present. The detection limit of thisquantitative RT-PCR assay was determined as two times the mean of thebackground signal. In this quantitative RT-PCR assay the detection limitcorresponded to 50 PCA3 RNA copies using 35 PCR amplification cycles.Since the saturation phase had the same effect on both targets (asdiscussed before), a calibration curve with a wide linear range thatextended from 50 to 1·10⁷ PCA3 RNA molecules was obtained (data notshown).

The reproducibility of the PCA3-based RT-PCR assay was established bythe comparison of four independent calibration curves. The dilutionseries of PCA3 and IS-PCA3 targets, the reverse transcription, PCR andhybridization assays of these four calibration curves were prepared andanalyzed in four independent assays. As can be concluded from thecombined calibration curve (data not shown), the overall intra-assayreproducibility is good with median coefficients of variation (CV) of 6%(range: 2-25%).

Quantification of PCA3 mRNA Expression in Tissue Specimens

The described PCA3-based RT-PCR assay was used to evaluate the potentialusefulness of PCA3 as a diagnostic marker for prostate cancer. Theprostate-specificity of PCA3 was determined by measuring the number ofPCA3 RNA copies in the cDNA obtained from several normal tissues ofbreast, bladder, duodenum, heart, liver, lung, kidney, prostate, seminalvesicle, skin, stomach, testis and peripheral blood leukocytes. Allsamples, except prostate, were negative for PCA3 (data not shown) whichwas in concordance with earlier published data (20;21).

Next, PCA3 RNA expression was determined in the following tissuespecimens: BPH (n=8), normal prostate (n=4), prostate tumor containingequal or less than 10% of prostate cancer cells (n=13) and prostatetumor containing more than 10% of prostate cancer cells (n=27) in orderto evaluate the usefulness of PCA3 as a prostate tumor marker. There wasno difference in the expression of PCA3 RNA between non-malignantprostate tissue and BPH tissue and therefore both were included in thegroup of non-malignant controls. In prostate tumors containing more than10% of prostate cancer cells, the median up-regulation of PCA3 was66-fold (median, 158.4·10⁵; range, 7.0·10⁵-994.0·10⁵) compared to thePCA3 expression in non-malignant controls (median, 2.4·10⁵; range0.2·10⁵-10.1·10⁵) (Table 4). Even in prostate tumors containing lessthan 10% of prostate cancer cells, the up-regulation of PCA3 expressionwas 11-fold (median 25.3·10⁵; range 6.6·10⁵-166.0·10⁵), as compared tothe expression in non-malignant controls. In 7 human radicalprostatectomy specimens the PCA3 expression in tumor areas was comparedto the PCA3 expression in the adjacent non-neoplastic prostate tissuefrom the same patients. Using the PCA3-based quantitative RT-PCR assay,6 to 1500-fold up-regulation of PCA3 was found in these prostate tumors,as compared to the adjacent non-neoplastic prostate tissue (Table 6).

For the determination of the potential diagnostic efficacy of thePCA3-based quantitative RT-PCR assay, a Receiver OperatingCharacteristic (ROC) curve was constructed (data not shown). The AreaUnder the Curve (AUC) was 0.98 (95% confidence interval, 0.94-1.01),indicating that the PCA3-based assay is very specific and has strongdiagnostic value.

Discussion

Currently RT-PCR is the most widely used method in the detection of asmall number of neoplastic cells in a large background of normal cells.In recent years, RT-PCR assays have been developed for theidentification of prostate cancer cells using PSA mRNA and PSMA mRNA asthe most commonly used targets for this technique (25;26;26-29). Many ofthese RT-PCR assays were qualitative, meaning that they providedinformation with respect to the presence or absence of these targets inthe PCR reaction products. Like all PCR assays, RT-PCR is an extremelysensitive assay. However, after the introduction of the nested RT-PCRmethod, PSA and PSMA transcripts were also detected in peripheral bloodleukocytes obtained from healthy donors (30;31). This indicates thatbasal transcripts of prostate-specific genes that might be present atlow background levels in non-prostate cells, could result in afalse-positive signal if the sensitivity of the RT-PCR technique becomestoo high. The background expression of many genes that earlier have beenconsidered as tissue or tumor-specific has contributed to the wide rangein sensitivity and specificity among the results of the RT-PCR studies.These contradictory results can be attributed to the lack of uniformityamong the used RT-PCR protocols. The background expression oftissue-specific genes does not invalidate their clinical use. However,it does imply that the development of more quantitative RT-PCRtechniques is necessary to obtain more reproducible and reliableresults.

In the detection and analyzes of RT-PCR products Southern blot followedby hybridization with specific radioactive oligonucleotide probesdominated the field of hybridization assays for two decades. Althoughsensitive, this technique is qualitative and time-consuming. In the pastdecade there has been a transition to non-radioactive alternativesbecause of the health hazards and the problems associated with the useand disposal of radioisotopes.

One of new technologies in the field of RT-PCR is the real-time PCRdetection of nucleic acids in a closed tube (32;33). This techniquedecreases the risk of contamination and it also simplifies the analysissince post-PCR hybridization steps are not required. Moreover, a largenumber of samples can be analyzed simultaneously. The method most widelyused for quantification is the generation of a calibration curve from adilution series of linearized plasmid containing the cDNA insert ofinterest. This dilution series is amplified in the same run as thesamples. Although widely used, this approach may have impact on theaccuracy of the assay. The RNA samples may be more prone to variationsin amplification efficiency that are caused by inhibitors present in thereverse transcribed sample compared to the amplification of the plasmidDNA (34). Because major variations are introduced in the reversetranscription step, the copy numbers obtained after real-time RT-PCR maynot reflect the copy number in the sample before cDNA synthesis. The useof an exogenous internal standard in both calibration curve and thesamples will correct for any differences that may occur during the cDNAsynthesis and could overcome this problem. However, in real-time PCRassays such a competitive internal standard cannot be used. Both targetand internal standard will compete for PCR reagents. If more than a10-fold difference exists between target and internal standard, then theless abundant species will not be amplified sufficiently for detection.This is because the more abundant target will consume most of the PCRreagents, especially the primers (34;35). To correct for thesesample-to-sample variations in real-time PCR a cellular RNA isRT-amplified simultaneously with the target RNA. These so-calledhousekeeping genes are used as an endogenous internal standard and theexpression of these genes should not vary in the tissues or cells underinvestigation or due to experimental treatment. These RNAs should alsobe expressed at about the same level as the target RNA. The number oftarget RNA copies is then normalized to the RNA expression of theabundant housekeeping gene. rRNAs may be useful as internal standardssince they are generated by a distinct polymerase (36). Therefore, theirexpression levels are not likely to vary under conditions that affectthe expression of RNAs (37). However, rRNAs are expressed at much higherlevels than the target RNA. Therefore, normalization of low abundanttarget RNA to the abundant housekeeping gene (e.g., 18 Svedberg Units(S) rRNA) might be difficult. This 18S rRNA is highly abundant comparedto the target mRNA transcripts. This makes it difficult to accuratelysubtract the baseline value in real-time RT-PCR data analysis (38). Toovercome these problems, Nurmi developed a target-like, non-competitive,exogenous internal standard for a real-time quantitative PSA assay (34).Omitting the IS from the analysis of PSA mRNA using real-time PCRresulted in a 172-fold underestimation of PSA RNA amount in a sample.Additionally, by using lanthanide-labeled probes instead of conventionalTaqMan™ probes, they were able to detect two separate targets even whenthe difference in their starting amounts is 100-fold. Due to thesuperior signal to noise ratio, the detection limit could be increasedby 10-fold. Using normal TaqMan™ probes and labels with rapidly decayingor prompt fluorescence, the detection limit was 1000 target mRNA copies,whereas the lanthanide-based detection was able to detect 100 PSA mRNAcopies. Although this development is still in a research-phase and thereis no real-time PCR instrument yet available for time-resolvedfluorescence detection this approach is a great improvement in real-timePCR for true quantifications of low expressed mRNAs.

In one embodiment it was decided not to use real-time PCR forquantification because of the earlier described problems in thecorrection for sample-to-sample preparation and accurate quantification.Therefore, a time-resolved fluorescence-based quantitative RT-PCR assayfor PCA3 was developed. Currently, time-resolved fluorescence (TRF) isconsidered as one of the most sensitive non-radioactive techniques thatallow to distinguish between the short lived prompt fluorescent signalobtained from the background of biological samples and the longfluorescent decay time of the lanthanide probes. Measurement of thelanthanide fluorescent signal does not occur until a certain time haselapsed from the moment of excitation. During this delay the short livedprompt fluorescent signal disappears, accounting for the highsensitivity of this technique (39). Ylikoski combined both techniques intheir time-resolved fluorescence-based quantitative RT-PCR assay for PSA(23;40). This provided a sensitive, quantitative and linear detection ofPSA mRNA in biological samples. The described time-resolvedfluorescence-based quantitative RT-PCR assay for PCA3 is based on theprinciple they have used.

As was discussed earlier, the most challenging problem associated withRT-PCR is the determination of the starting quantity of target RNA. Forquantification of PCA3, a constant amount of exogenous internal RNAstandard was added to each sample and to each of the calibratorscovering the wide linear range of 50 to 1·10⁷ PCA3 RNA copies. ThisIS-PCA3 only contained a 3 bp difference with respect to the PCA3 mRNA.The internal standard was added to the sample prior to cDNA synthesis.Therefore, it can correct for variations during the entire assayprocedure from reverse transcription to the detection of amplificationproducts by the hybridization assay. We have shown that both targetswere equally co-amplified because of their resemblance in size andsequence. The small difference in sequence allowed the construction oftwo specific hybridization probes for the detection of PCA3 and IS-PCA3.The conditions for the hybridization have been optimized to avoidcross-hybridization between the probes and their targets. We have shownthat the two targets were selectively detected by the probes in thehybridization assay. The probes were labelled with two differentlanthanides, europium and terbium. The sharp emission peaks and thedifferent decay times of Eu³⁺ and Tb³⁴ allow the simultaneous detectionof both analytes in one microtiter well. To determine the startingquantity of PCA3 mRNA in a sample, the fluorescence PCA3/IS-PCA3 ratioobtained from the sample was compared to the ratios obtained for thecalibrators. This dual-label TRF-based hybridization assay in microtiterplates allows the quantification of PCA3 mRNA in a large number ofsamples with only a single set of twelve calibrators. Moreover, theintra-assay reproducibility is good with median coefficients ofvariation (CV) of 6% (range 2-25%). Using this method, up to 50 PCA3copies could be detected when they were co-amplified with 100-fold more(5000 copies) of internal standard. This would not have been possibleusing the conventional real-time PCR technique since a more than 10-folddifference between target and internal standard would lead to aninsufficient amplification of the less abundant species. The sensitivityof this technique becomes important in a diagnostic setting where smallquantities of the sequence of interest have to be detected. Thetime-resolved fluorescence-based quantitative RT-PCR method described isquantitative, more sensitive, faster and easier than the conventionalanalysis based on Southern blotting and membrane hybridization.

The herein described time-resolved fluorescence-based quantitativeRT-PCR assay for PCA3 showed that PCA3 was exclusively expressed in theprostate. This was in concordance with earlier published data (20;21).This quantitative RT-PCR assay obtained AUC-ROC values of 0.98 for PCA3.It demonstrates the high discrimination power of this transcript todifferentiate between malignant and non-malignant prostate tissues.Bussemakers and colleagues found a 10-100 fold over-expression of PCA3in tumor areas compared to adjacent non-neoplastic prostate tissue basedon Northern blot analysis. Using this quantitative time-resolvedfluorescence-based assay we showed that the PCA3 expression in tumorareas of the radical prostatectomy specimens of 7 patients wasup-regulated 6 to 1500-fold compared to the adjacent non-neoplasticprostate tissue. In the non-matched group of tissue specimens a median66-fold up regulation of PCA3 was found in the prostate tumorscontaining more than 10% of tumor cells. The median up-regulation ofPCA3 of 11-fold in prostate tissue samples containing less than 10% oftumor cells indicates that the PCA3 assay is capable of detecting a fewmalignant cells in a background of predominantly non-malignant cells.These data were in concordance with the data obtained from the recentlydeveloped real-time PCR assay (21).

The combined data and the fact that PCA3 is not expressed in leukocytes(often present in bodily fluids) indicate that quantitative RT-PCR assayfor PCA3 bears great promise as diagnostic tool. As such it could beapplicable in the detection of malignant prostate cells in blood, urineor ejaculates obtained from patients who are suspected of havingprostate cancer. Recently, this hypothesis was tested by Hessels (Eur.Urol. 2003 supra) using the herein described molecular test to analyzeurinary sediments after thorough digital rectal examination of theprostate. The combined data showed that the quantitative determinationof PCA3 transcripts in urinary sediments obtained after extensiveprostate massage, has high specificity (83%) compared to serum PSA (20%)for the detection of prostate cancer. Moreover, the negative predictivevalue of this test was 90%. Therefore, it bears great potential in thereduction of the number of biopsies.

Herein a very sensitive time-resolved fluorescence-based quantitativeRT-PCR assay with a wide linear detection range of 50 to 1·10⁷ PCA3copies was developed. In this assay, the target-like exogenous internalstandard controls for sample-to-sample variations from the cDNAsynthesis to the hybridization assay. This assay has shown that PCA3 canhighly discriminate between malignant and non-malignant prostatetissues. We recently showed that this quantitative RT-PCR assay isapplicable to the detection of prostate cancer cells in urine sediments.Thus, multicenter studies using validated PCA3 assays, can provide thefirst basis for the utility of molecular diagnostics in clinicalurological practise.

The potential diagnostic efficacy of the PCA3-based assay was determinedby quantitative measurement of PCA3 transcripts in non-malignant andmalignant prostate specimens. Before the reverse-transcription reaction,total RNA obtained from normal prostate and prostate cancer tissuespecimens was mixed with an exogenous PCA3-like internal RNA standard.This internal standard corrects for variations during the entire assayprocedure. After RT-PCR co-amplification of PCA3 and the internalstandard, the samples were immobilized on streptavidin-coated microtiterwells. Each target was hybridized to a specific probe, labeled witheither europium or terbium. Time-resolved fluorometry was used for themeasurement of these strongly fluorescent lanthanide chelates. Thequantification of PCA3 mRNA copies in a sample was determined from acalibration curve covering the wide linear range of 50 to 1·10⁷ PCA3copies

Prostate tumors showed a 66-fold up-regulation of PCA3 (median 158.4·10⁵copies/μg tissue RNA) when compared to benign prostate tissue (median2.4·10⁵ copies/μg tissue RNA). This up-regulation was found in more than95% of prostate cancer specimens studied. The herein presented datarevealed that tissue specimens containing less than 10% of cancer cellscould be accurately discriminated from non-malignant specimens. Hence,detection of a small fraction of prostate cancer cells in a backgroundof normal cells seems feasible. The diagnostic efficacy of thePCA3-based assay was visualized in a receiver operating characteristiccurve. The area under curve of 0.98 (95% CI: 0.94-1.01) confirmed theexcellent discrimination power of this assay. The quantitative RT-PCRassay for PCA3 described, bears great promise as a tool to be used forprostate cancer prognosis (and diagnosis).

Recently, a number of prostate-specific genes have been identified suchas prostate-specific membrane antigen (PSMA) (12), NKX3.1 (13), prostatestem cell antigen (PSCA) (14), prostate tumor inducing gene-1 (PTI-1)(15), PCGEM-1 (16), PDEF (17), TMPRSS2 (18) and Prostase (19). However,diagnoses based on the expression of these prostate-specific genes hasnot been described. In addition, the most promising candidate for adiagnostic screening test remains the prostate-specific PCA3 gene sinceits expression is restricted to the prostate and is stronglyup-regulated in more than 95% of primary prostate cancers (20;21). Tofurther demonstrate the potential usefulness of PCA3 as a diagnosticmarker for prostate cancer, a time-resolved fluorescence-basedquantitative RT-PCR assay (using an exogenous internal standard and anexternal calibration curve) was developed. The sensitivity andspecificity of this time-resolved fluorescence-based quantitative RT-PCRassay for PCA3 was validated using a large panel of well-characterizednormal and malignant prostate specimens.

Although the present invention has been described hereinabove by way ofpreferred embodiments thereof, it can be modified, without departingfrom the spirit and nature of the subject invention as defined in theappended claims.

TABLE 2 PCA3 NUCLEIC ACID PRIMERS Nucleic Acid Region Size NucleotidesSize Nucleotides Exon Sequence from Which to Derive Primers Exon 1 98  1-98 of SEQ ID NO: 1 120   1-120 of SEQ ID NO: 2 Exon 2 165  99-263 ofSEQ ID NO: 1 165  121-285 of SEQ ID NO: 2 Exon 3 183 264-446 of SEQ IDNO: 1 183  286-468 of SEQ ID NO: 2 Exon 4a 539 447-985 of SEQ ID NO: 1539  469-1007 of SEQ ID NO: 2 Exon 4b 1052 986-2037 of SEQ ID NO: 1 1059 1008-2066 of SEQ ID NO: 2 Exon 4c — — 556 2067-2622 of SEQ ID NO: 2Exon 4d — — 960 2623-3582 of SEQ ID NO: 2 Exon Junction Specific PrimersExon Junction 1 20  89-108 of SEQ ID NO: 1 20  109-128 of SEQ ID NO: 2(SEQ ID NO: 5) (SEQ ID NO: 6) Exon Junction 2 20 252-271 of SEQ ID NO: 120  274-293 of SEQ ID NO: 2 (SEQ ID NO: 7) (SEQ ID NO: 7)

TABLE 3 PCA3 NUCLEIC ACID PROBES SEQ ID Size Nucleotides Sequence NO: 20  1-20 of SEQ ID NO: 1 AGAAGCTGGCATCAGAAAAA 12 30   1-30 of SEQ ID NO: 1AGAAGCTGGCATCAGAAAAACAGAGGGGAG 13 40   1-40 of SEQ ID NO: 1AGAAGCTGGCATCAGAAAAACAGAGGGGAG 14 ATTTGTGTGG 20  89-108 of SEQ ID NO: 1TGATACAGAGGAATTACAAC  5 30 257-286 of SEQ ID NO: 1GGCAGGGGTGAGAAATAAGAAAGGCTGCTG 15 20 274-293 of SEQ ID NO: 1AGAAAGGCTGCTGACTTTAC 16 20   1-20 of SEQ ID NO: 2 ACAGAAGAAATAGCAAGTGC17 30   1-30 of SEQ ID NO: 2 ACAGAAGAAATAGCAAGTGCCGAGAAGCTG 18 40  1-40 of SEQ ID NO: 2 ACAGAAGAAATAGCAAGTGCCGAGAAGCTG 19 GCATCAGAAA 30114-143 of SEQ ID NO: 2 TACAGAGGAATTACAACACATATACTTAGT 20 20284-303 of SEQ ID NO: 2 GGGTGAGAAATAAGAAAGGC 21

TABLE 4 Exon  Primer SEQ Junction Pairs in ID Detected PCA3 ExonsExon Junction Probes NO: Exon 1/ exon 1 and GGACCTGATGATACAGAGGAATTAC 22exon 2 exon 2 Exon 1/ exon 1 and GAGGAATTACAACAC 23 exon 2 exon 2Exon 1/ exon 1 and GATGATACAGAGGAATTACAACAC 24 exon 2 exon 2 Exon 1/exon 1 and GATGATACAGAGGTGAGAAATAAG 25 exon 3 exon 3 Exon 1/ exon 1 andCAGAGGTGAGAAATAAGAAAGGC 26 exon 3 exon 3 Exon 1/ exon 1 andGATACAGAGGTGAGAAATAAG 27 exon 3 exon 3 Exon 1/ exon 1 andGATACAGAGGTGAGAAATAAGAAAGGC 28 exon 3 exon 3 TGCTGAC Exon 2/ exon 2 andGGCAGGGGTGAGAAATAAG 29 exon 3 exon 3, or exon 1 and exon 3 Exon 2/exon 2 and CTCAATGGCAGGGGTGAG 30 exon 3 exon 3, or exon 1 and exon 3Exon 2/ exon 2 and CTCAATGGCAGGGGTGAGAAATAAGAA 31 exon 3 exon 3, orAGGCTGCTGAC exon 1 and exon 3 Exon 3/ exon 3 and GGAAGCACAGAGATCCCTGG  8exon 4 exon 4, or exon 1 and exon 4, or exon 2 and exon 4 Exon 3/exon 3 and GCACAAAAGGAAGCACAGAGATCCCTG 32 exon 4 exon 4, or GGAGexon 1 and exon 4, or exon 2 and exon 4 Exon 3/ exon 3 andGCACAGAGATCCCTGGGAG 33 exon 4 exon 4, or exon 1 and exon 4, orexon 2 and exon 4 Exon 3/ exon 3 and GCACAGAGGACCCTTCGTG 34 exon 4exon 4, or exon 1 and exon 4, or exon 2 and exon 4 Exon 3/ exon 3 andGGAAGCACAAAAGGAAGCACAGAGATC 35 exon 4 exon 4, or CCTGGG exon 1 andexon 4, or exon 2 and exon 4

TABLE 5 PCA3 mRNA expression in normal prostate, BPH and prostate tumorsamples PCA3 mRNA Gleason copies/ug Sample Pathology % PCa score tissueRNA (×1 · 10⁵) non-malignant controls 198 BPH 0.15 162 BPH 0.20 124 BPH0.34 153 BPH 0.39 127 BPH 0.72 120 NPr 1.79 669 BPH 3.03 663 NPr 3.14327 BPH 7.12 234 BPH/NPr 7.39 674 NPr 7.56 128 NPr 10.06 median 2.41≦10% PCa 193 Tumor 5 6 6.55 676 Tumor 6 6 7.23 328 Tumor focal 6 12.68665 Tumor focal 6 14.05 161 Tumor focal 6 14.07 238 Tumor 5 7 19.87 122Tumor 1 6 25.32 158 Tumor 10 6 32.01 668 Tumor 5 6 55.95 203 Tumor 5 760.56 195 Tumor focal 6 85.88 661 Tumor 5 6 114.19 675 Tumor 10 6 165.95median 25.32 >10% Pca 715 Tumor 20 7 7.02 126 Tumor 40 6 11.32 143Tumor >10% 7 16.30 707 Tumor 80 5 19.17 744 Tumor 30 7 34.16 129 Tumor80 8 59.12 121 Tumor 90 8 61.55 673 Tumor 90 5 62.94 713 Tumor 70 375.62 29 Tumor 80 5 77.89 704 Tumor 85 6 89.20 237 Tumor 80 5 115.58 667Tumor 65 6 138.50 717 Tumor 40 7 158.43 710 Tumor 20 7 215.89 48 Tumor95 10 217.12 194 Tumor 80 6 221.17 147 Tumor >10% 6 249.99 118 Tumor 678 264.77 709 Tumor 30 6 270.77 664 Tumor 60 8 296.48 163 Tumor 90 6297.25 145 Tumor >10% 7 305.98 662 Tumor 70 6 487.88 666 Tumor 60 5536.21 141 Tumor >10% 7 663.86 235 Tumor 80 7 993.99 median 158.43 BPH:Benign Prostatic Hyperplasia PCa: prostate cancer NPr: normal prostate

TABLE 6 Comparison of PCA3 mRNA expression between non- malignantprostate and prostate tumor tissue of the same patient PCA3 mRNAcopies/□g tissue RNA (×1 · 10⁴) Sample code Ratio Patient NPr PCa NPrPCa T/N 1 128 129 100 590 6 2 674 673 76 630 8 3 127 126 7 113 16 4 663664 31 2965 96 5 234 235 74 9940 134 6 120 118 18 2648 147 7 162 163 22973 1487 NPr: normal prostate tissue PCa: prostate tumor tissue

TABLE 7 PA Conclusion patient PSA RNA PCA3 PSA Ratio PA biopsy DiagnosisRRP RRP 1 4.23 946 974 12054 81 T03-11049 no malignancy , 87 6.68 1076118 33359 4 T04-00507 no malignancy , 137 , 1166 211 5272 40 T03-05862no malignancy , 164 4.6 1216 0 23003 0 T04-04972 no malignancy , 92 4.411081 82 936 87 T04-00521 no malignancy , 150 4.83 1184 68 151 451T04-04416 no malignancy , 178 3.52 1242 0 9387 0 T04-05581 no malignancy, 118 6.07 1119 0 884 0 T04-01860 no malignancy , 196 7.91 1272 166 986168 T04-07086 no malignancy , 11 , 923 168 1408 119 T03-09658 nomalignancy , 11 , 926 166 16799 10 T03-09658 no malignancy , 12 23.281105 177 10414 17 T04-00849 no malignancy , 13 4.7 988 0 2926 0T03-12238 no malignancy , 77 6.9 1050 133 3696 36 T03-14332 nomalignancy , 113 , 1114 122 277 441 T03-03241 no malignancy , 14 5.9 99723729 21318 1113 T03-12798 no malignancy , 127 4.92 1153 58 6128 9T04-04409 no malignancy , 15 6.9 935 1239 13184 94 T03-09652 nomalignancy , 151 5.1 1188 988 1580 625 T04-05305 no malignancy , 16 4.44919 557 1888 295 T03-09660 no malignancy , 16 2.2 1276 128 635 202T03-09660 no malignancy , 17 7.6 925 143 1333 107 T03-09656 nomalignancy , 139 9.55 1169 98 1930 51 T03-08073 no malignancy , 18 26.8985 177 2632 67 T03-12252 no malignancy , 68 17.9 1018 185 3008 62T03-14038 no malignancy , 68 13.82 1044 267 5614 48 T03-14038 nomalignancy , 112 7.17 1113 2145 10119 212 T04-00842 no malignancy , 1119.46 1112 0 712 0 T04-01175 no malignancy , 200 17.7 1256 0 1318 0T04-06474 no malignancy , 129 1.08 1158 0 1396 0 T04-02170 no malignancy, 149 8.1 1195 295 4992 59 T04-03473 no malignancy , 130 32 1159 78 153651 T04-04418 no malignancy , 97 7.86 1068 901 7204 125 T03-12795 nomalignancy , 62 8.55 1010 0 1840 0 T03-13081 no malignancy , 20 0.93 9421008 1960 518 T03-10730 no malignancy , 21 10 991 223 17451 13 T03-04605no malignancy , 140 49.57 1170 283 5439 52 T03-03313 no malignancy , 235.68 992 0 3631 0 T03-12531 no malignancy , 26 1.19 989 922 19742 47T03-12529 no malignancy , 27 5.4 960 222 1531 145 T03-11915 nomalignancy , 29 5.41 993 102 11858 9 T03-12533 no malignancy , 31 6.71940 4703 39511 120 T03-10448 no malignancy , 73 7.5 1024 372 20984 18T03-14028 no malignancy , 76 8.35 1043 62 369 168 T03-14034 nomalignancy , 198 6.74 1274 234 3066 76 T04-06256 no malignancy , 13210.35 1161 121 1360 89 T04-02172 no malignancy , 64 14.14 1014 204 706289 T04-04966 no malignancy , 64 14.14 1217 552 24878 22 T04-04966 nomalignancy , 64 14.14 1244 1011 18431 55 T04-05575 no malignancy , 13310.85 1162 7392 56456 131 T04-02178 no malignancy , 133 22.6 1167 258012569 205 T04-02178 no malignancy , 104 6.41 1104 780 1884 414 T04-00851no malignancy , 33 11.3 938 0 1413 0 T03-10446 no malignancy , 93 7.181082 1824 6645 274 T04-00518 no malignancy , 110 8.12 1111 0 1686 0T04-01183 no malignancy , 157 3.36 1209 0 23685 0 T04-04650 nomalignancy , 119 11.74 1120 253 3352 75 T04-01539 no malignancy , 13413.02 1163 1042 23137 45 T04-02176 no malignancy , 170 5.04 1225 1075682 19 T04-04646 no malignancy , 82 5.07 1046 1048 1719 610 T03-14338no malignancy , 59 4.79 1006 6989 37995 184 T03-13078 no malignancy ,182 6.8 1238 477 34720 14 T04-05369 no malignancy , 96 5.3 1071 433666786 65 T03-13415 no malignancy , 181 4.95 1239 0 10403 0 T04-05302 nomalignancy , 98 5.57 1098 58 1293 44 T04-00820 no malignancy , 194 4.181270 120 14280 8 T04-06754 no malignancy , 201 4.8 1257 639 25343 25T03-14641 no malignancy , 103 7.73 1103 0 550 0 T04-00846 no malignancy, 101 , 1277 0 505 0 T03-14040 no malignancy , 126 10.76 1152 0 11523 0T04-01855 no malignancy , 46 12.91 983 235 14462 16 T03-14639 nomalignancy , 47 13.9 944 7509 32691 230 T03-13435 no malignancy , 1635.99 1215 0 41990 0 T04-04968 no malignancy , 147 16 1181 487 14526 34T04-04422 no malignancy , 191 6.6 1267 511 2740 186 T04-00267 nomalignancy , 171 6.82 1226 512 2647 193 T04-04643 no malignancy , 123 241138 0 8052 0 T04-03121 no malignancy , 50 5.17 941 780 7358 107T03-10732 no malignancy , 52 , 996 609 17412 35 T03-12800 no malignancy, 80 3.53 1048 352 8416 42 T03-14330 no malignancy , 55 , 984 73 3419 21T03-13126 no malignancy , 174 10.38 1230 960 22230 43 T04-04407 nomalignancy , 70 , 1021 93 98251 1 T03-13720 no malignancy , 56 29 982 0940 0 T03-14334 no malignancy , 56 29.08 1005 82 471 174 T04-04413 nomalignancy , 75 8.68 1026 115 3118 37 T03-14030 no malignancy , 136 4.81165 0 22843 0 T04-02788 no malignancy , 193 4.21 1269 284 15158 19T04-06729 Gleason 6 , 4 5 998 13549 37999 357 T04-06172 Gleason 7Gleason pT2AN0R1 4 + 3 = 7 190 12.02 1265 55 845 65 T04-06728 Gleason 7, 186 4.94 1261 48 129 372 T04-06470 Gleason 6 , 8 , 947 252 635 397Gleason 5 , 122 6.24 1123 366 430 852 T04-01537 Gleason 6 GleasonpT2BN0R1 3 + 3 = 6 9 6.25 932 , , 136 T03-10189 Gleason 6 , 9 6.25 9322141 8222 260 T03-10189 Gleason 6 , 91 4.49 1078 401 1689 237 T04-00510Gleason 6 , 66 5.3 1016 534 6623 81 T03-13432 Gleason 6 Gleason pT2AN0R03 + 3 = 6 63 30.4 1012 1640 3781 434 T03-13436 Gleason 7 , 166 6.42 1221116 6178 19 T04-04967 Gleason 6 , 19 62 933 , , 222 T03-09755 Gleason 8Gleason pT4N1 4 + 4 = 8 19 62 933 392329 704960 577 T03-09755 Gleason 8Gleason pT4N1 4 + 4 = 8 65 4.23 1015 103 1180 87 T04-02391 Gleason 6Gleason pT2CN0R1 2 + 4 = 6 195 17.62 1271 137 402 340 T04-06731 Gleason7 , 25 7.1 963 1031 1038 1012 T04-01468 Gleason 7 Gleason pT2AN0R1 3 + 4= 7 192 8.93 1268 5610 37695 149 T04-06730 Gleason 7 , 120 9.77 1121 77510035 77 T04-01533 Gleason 7 , 30 7.49 965 291 6414 46 T03-11922 Gleason6 , 167 24 1222 395 2254 175 T04-06472 Gleason 7 , 32 , 928 102 429 243T03-11626 Gleason 6 , 32 , 928 594 518 1147 T03-11626 Gleason 6 , 7985.63 1049 122 223 547 T03-14340 Gleason 9 , 143 5.1 1219 0 7351 0T04-06258 Gleason 6 , 109 30 1110 1072 6302 170 T04-06287 Gleason 9Gleason pT3AN0R1 4 + 5 = 9 34 9.56 990 1375 12730 108 T03-12527 Gleason6 , 169 3.52 1224 15610 23584 662 T04-04644 Gleason 6 , 172 11.53 12273409 7448 458 T04-04652 Gleason 6 , 142 9.06 1218 163 3924 41 T04-06400Gleason 5 Gleason pT2CN0R0 2 + 3 = 5 57 7.55 1003 251 7094 35 T03-13075Gleason 6 , 162 1 1214 109 578 189 T04-04964 Gleason 6 , 125 11.61 1151228 564 404 T04-00822 Gleason 7 Gleason pT3AN0R1 4 + 3 = 7 154 6.9 119980 379 211 T04-04180 Gleason 6 , 154 6.9 1229 224 711 315 T04-04180Gleason 6 , 155 5.38 1207 0 3913 0 T04-04877 Gleason 5 , 90 9.45 10773511 16621 211 T04-00516 Gleason 7 , 100 7.18 1100 404 9690 42 T04-01181Gleason 6 , 156 5.52 1208 431 43117 10 T04-06076 Gleason 5 Gleasonpt2AN0R0 2 + 3 = 5 153 10.33 1189 355 1549 229 T04-03468 Gleason 6 , 1215.98 1122 424 3787 112 T04-01531 Gleason 4 , 121 5.98 1122 773 5508 140T04-01531 Gleason 7 Gleason pT3BN0R0 4 + 3 = 7 173 6.66 1228 189 1684112 T04-04183 Gleason 6 , 72 15.7 1023 209 1345 155 T04-03591 Gleason 7Gleason pT3AN0R0 4 + 3 = 7 117 9.38 1118 6056 12872 470 T04-06788Gleason 7 Gleason pT3AN0R1 3 + 4 = 7 183 21.24 1236 10259 121054 85T04-05303 Gleason 6 , 94 12.28 1080 789 9888 80 T04-00527 Gleason 9 ,184 3.9 1259 57 57 1000 T04-07087 Gleason 8 , 61 25.27 1013 587 4354 135T03-13417 Gleason 7 ,

REFERENCES

-   1. Jensen O M, Esteve J, Moller H, Renard H. Cancer in the European    Community and its member states. Eur J Cancer 1990; 26:1167-256.-   2. Beduschi M C, Oesterling J E. Percent free prostate-specific    antigen: the next frontier in prostate-specific antigen testing.    Urology 1998; 51:98-109.-   3. Brawer M K, Chetner M P, Beatie J, Buchner D M, Vessella R L,    Lange P H. Screening for prostatic carcinoma with prostate specific    antigen. J Urol 1992; 147:841-5.-   4. Catalona W J, Smith D S, Ratliff T L, Dodds K M, Coplen D E, Yuan    J J et al. Measurement of prostate-specific antigen in serum as a    screening test for prostate cancer. N Engl J Med 1991; 324:1156-61.-   5. Brawer M K. Prostate-specific antigen. Semin Surg Oncol 2000;    18:3-9.-   6. Nixon R G, Brawer M K. Enhancing the specificity of    prostate-specific antigen (PSA): an overview of PSA density,    velocity and age-specific reference ranges. Br J Urol 1997; 79 Suppl    1:61-7:61-7.-   7. Polascik T J, Oesterling J E, Partin A W. Prostate specific    antigen: a decade of discovery-what we have learned and where we are    going. J Urol 1999; 162:293-306.-   8. Kamoi K, Babaian R J. Advances in the application of    prostate-specific antigen in the detection of early-stage prostate    cancer. Semin Oncol 1999; 26:140-9.-   9. Nixon R G, Brawer M K. Enhancing the specificity of    prostate-specific antigen (PSA): an overview of PSA density,    velocity and age-specific reference ranges. Br J Urol 1997; 79 Suppl    1:61-7:61-7.-   10. Ukimura O, Durrani O, Babaian R J. Role of PSA and its indices    in determining the need for repeat prostate biopsies. Urology 1997;    50:66-72.-   11. Mettlin C J, Murphy G P, Ho R, Menck H R. The National Cancer    Data Base report on longitudinal observations on prostate cancer.    Cancer 1996; 77:2162-6.-   12. Murphy G P, Barren R J, Erickson S J, Bowes V A, Wolfert R L,    Bartsch G et al. Evaluation and comparison of two new prostate    carcinoma markers. Free-prostate specific antigen and prostate    specific membrane antigen. Cancer 1996; 78:809-18.-   13. Xu L L, Srikantan V, Sesterhenn I A, Augustus M, Dean R, Moul J    W et al. Expression profile of an androgen regulated prostate    specific homeobox gene NKX3.1 in primary prostate cancer. J Urol    2000; 163:972-9.-   14. Gu Z, Thomas G, Yamashiro J, Shintaku I P, Dorey F, Raitano A et    al. Prostate stem cell antigen (PSCA) expression increases with high    gleason score, advanced stage and bone metastasis in prostate    cancer. Oncogene 2000; 19:1288-96.-   15. Sun Y, Lin J, Katz A E, Fisher P B. Human prostatic carcinoma    oncogene PTI-1 is expressed in human tumor cell lines and prostate    carcinoma patient blood samples. Cancer Res 1997:57:18-23.-   16. Srikantan V, Zou Z, Petrovics G, Xu L, Augustus M, Davis L et    al. PCGEM1, a prostate-specific gene, is overexpressed in prostate    cancer. Proc Natl Acad Sci USA 2000 Oct. 24; 97(22):12216-21 2001;    97:12216-21.-   17. Oettgen P, Finger E, Sun Z, Akbarali Y, Thamrongsak U, Boltax J    et al. PDEF, a novel prostate epithelium-specific ets transcription    factor, interacts with the androgen receptor and activates    prostate-specific antigen gene expression. J Biol Chem 2000;    275:1216-25.-   18. Lin B, Ferguson C, White J T, Wang S, Vessella R, True L D et    al. Prostate-localized and androgen-regulated expression of the    membrane-bound serine protease TMPRSS2. Cancer Res 1999; 59:4180-4.-   19. Nelson P S, Gan L, Ferguson C, Moss P, Gelinas R, Hood L,    Wang K. Molecular cloning and characterization of prostase, an    androgen-regulated serine protease with prostate-restricted    expression. Proc Nati Acad Sci USA 1999; 96:3114-9.-   20. Bussemakers M J, van Bokhoven A, Verhaegh G W, Smit F P,    Karthaus H F, Schalken J A et al. DD3: a new prostate-specific gene,    highly overexpressed in prostate cancer. Cancer Res 1999; 59:5975-9.-   21. de Kok J B, Verhaegh G W, Roelofs R W, Hessels D, Kiemeney L A,    Aalders T W et al. DD3(PCA3), a very sensitive and specific marker    to detect prostate tumors. Cancer Res 2002; 62:2695-8.-   22. Auffray C, Rougeon F. Purification of mouse immunoglobulin    heavy-chain messenger RNAs from total myeloma tumor RNA. Eur J    Biochem 1980; 107:303-14.-   23. Ylikoski A, Sjoroos M, Lundwall A, Karp M, Lovgren T, Lilja H,    litia A. Quantitative reverse transcription-PCR assay with an    internal standard for the detection of prostate-specific antigen    mRNA. Clin Chem 1999; 45:1397-407.-   24. Raeymaekers L. Quantitative PCR: theoretical considerations with    practical implications. Anal Biochem 1993; 214:582-5.-   25. Grasso Y Z, Gupta M K, Levin H S, Zippe C D, Klein E A. Combined    nested RT-PCR assay for prostate-specific antigen and    prostate-specific membrane antigen in prostate cancer patients:    correlation with pathological stage. Cancer Res 1998; 58:1456-9.-   26. Ferrari A C, Stone N N, Eyler J N, Gao M, Mandeli J, Unger P et    al. Prospective analysis of prostate-specific markers in pelvic    lymph nodes of patients with high-risk prostate cancer. J Natl    Cancer Inst 1997; 89:1498-504.-   27. Goldman H B, Israeli R S, Lu Y, Lemer J L, Hollabaugh R S,    Steiner M S. Can prostate-specific antigen reverse    transcriptase-polymerase chain reaction be used as a prospective    test to diagnose prostate cancer? World J Urol 1997; 15:257-61.-   28. Katz A E, de Vries G M, Begg M D, Raffo A J, Cama C, O'Toole K    et al. Enhanced reverse transcriptase-polymerase chain reaction for    prostate specific antigen as an indicator of true pathologic stage    in patients with prostate cancer. Cancer 1995; 75:1642-8.-   29. Katz A E, Olsson C A, Raffo A J, Cama C, Perlman H, Seaman E et    al. Molecular staging of prostate cancer with the use of an enhanced    reverse transcriptase-PCR assay. Urology 1994; 43:765-75.-   30. Smith M R, Biggar S, Hussain M. Prostate-specific antigen    messenger RNA is expressed in non-prostate cells: implications for    detection of micrometastases. Cancer Res 1995; 55:2640-4.-   31. Lintula S, Stenman U H. The expression of prostate-specific    membrane antigen in peripheral blood leukocytes. J Urol 1997;    157:1969-72.-   32. Bustin S A. Absolute quantification of mRNA using real-time    reverse transcription polymerase chain reaction assays. J Mol    Endocrinol 2000; 25:169-93.-   33. Bernard P S, Wittwer C T. Real-time PCR technology for cancer    diagnostics. Clin Chem 2002; 48:1178-85.-   34. Nurmi J, Wikman T, Karp M, Lovgren T. High-performance real-time    quantitative RT-PCR using lanthanide probes and a dual-temperature    hybridization assay. Anal Chem 2002; 74:3525-32.-   35. Gibson U E, Heid C A, Williams P M. A novel method for real time    quantitative RT-PCR. Genome Res 1996; 6:995-1001.-   36. Paule M R, White R J. Survey and summary: transcription by RNA    polymerases I and III. Nucleic Acids Res 2000; 28:1283-98.-   37. Barbu V, Dautry F. Northern blot normalization with a 28S rRNA    oligonucleotide probe. Nucleic Acids Res 1989; 17:7115.-   38. Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De    Paepe A, Speleman F. Accurate normalization of real-time    quantitative RT-PCR data by geometric averaging of multiple internal    control genes. Genome Biol 2002; 3: RESEARCH0034.-   39. Soini E, Lovgren T. Time-resolved fluorescence of lanthanide    probes and applications in biotechnology. CRC Crit Rev Anal Chem    1987; 18:105-54.-   40. Ylikoski A, Karp M, Lilja H, Lovgren T. Dual-label detection of    amplified products in quantitative RT-PCR assay using    lanthanide-labeled probes. Biotechniques 2001:30:832-6, 838, 840.

1-26. (canceled)
 27. A method for characterizing prostate cancer in a biological sample of a subject comprising: a) synthesizing PCA3 cDNA from a prostate cancer specific PCA3 mRNA from the biological sample; b) measuring the amount of the synthesized PCA3 cDNA; c) measuring an amount of PSA in the biological sample; and d) determining a ratio value of the amount of the synthesized PCA3 cDNA over the amount of PSA.
 28. The method of claim 27, further comprising comparing the ratio value to at least one predetermined cut-off value.
 29. The method of claim 28, wherein a ratio value above the predetermined cut-off value is indicative of a higher risk of mortality of prostate cancer as compared to a ratio value below the predetermined cut-off value; or of the presence of a more aggressive cancer as compared to a ratio value below the predetermined cut-off value which is indicative of the presence of a less aggressive cancer.
 30. The method of claim 28, wherein a ratio value above the predetermined cut-off value is indicative of a greater prostate cancer tumor volume as compared to a ratio value below the predetermined cut-off value; or of a more advanced stage of prostate cancer as compared to a ratio value below the predetermined cut-off value.
 31. The method of claim 27, wherein the ratio value is useful for estimating or determining a grade or stage of prostate cancer.
 32. The method of claim 27, wherein the biological sample comprises urine, resected prostate tissue, biopsied prostate tissue, ejaculate, or a bladder washing.
 33. The method of claim 27, wherein the amount of PSA is the amount of PSA mRNA.
 34. The method of claim 27, wherein the PCA3 cDNA is synthesized in an amplification reaction.
 35. The method of claim 34, wherein the amplification reaction comprises RT-PCR, transcription mediated amplification, nucleic acid sequence-based amplification, or strand displacement amplification.
 36. The method of claim 27, wherein the amount of PSA is the amount of PSA protein.
 37. The method of claim 27, wherein the biological sample is obtained from a patient undergoing a prostate cancer treatment.
 38. The method of claim 37, wherein the ratio value is used to determine an effect of the treatment on the cancer or mortality risk.
 39. The method of claim 27, wherein the subject has a serum PSA protein level of at least about 3 ng/ml.
 40. A method for characterizing prostate cancer in a biological sample comprising: a) contacting a biological sample with one or more first oligonucleotides that hybridize to a prostate cancer specific PCA3 mRNA or a complement thereof; b) contacting the biological sample with one or more second oligonucleotides that hybridize to a PSA mRNA or a complement thereof; c) determining the amount of PCA3 mRNA and the amount of PSA mRNA present in the biological sample; d) determining a ratio value of the amount of PCA3 mRNA over the amount of PSA mRNA, wherein the one or more first oligonucleotides comprise at least one of an artificially labeled oligonucleotide or a promoter-primer.
 41. The method of claim 40, wherein the one or more first oligonucleotides comprise at least one oligonucleotide artificially labeled with a fluorescent, colorimetric, enzymatic, enzyme substrate, radioactive, bioluminescent, phosphorescent, affinity ligand, or homogeneous detectable label.
 42. The method of claim 40, wherein the one or more first oligonucleotides comprise at least one promoter-primer.
 43. The method of claim 40, wherein the one or more first oligonucleotides are used to amplify the prostate cancer specific PCA3 mRNA or complement thereof.
 44. The method of claim 43, wherein the amplification reaction comprises polymerase chain reaction (PCR); nucleic acid sequence-based amplification assay (NASBA); transcription mediated amplification (TMA); ligase chain reaction (LCR); or strand displacement amplification (SDA).
 45. The method of claim 40, wherein the amounts of the prostate cancer specific PCA3 nucleic acid and of the PSA nucleic acid are determined using a hybridization assay.
 46. The method of claim 40, wherein the promoter-primer or artificially labeled oligonucleotide hybridizes to a PCA3 nucleic acid sequence comprising (i) the nucleic acid sequence set forth in SEQ ID NO:1; (ii) the nucleic acid sequence set forth in SEQ ID NO:2; or (iii) a nucleic acid sequence that hybridizes under high stringency conditions to a nucleic acid sequence in (i) or (ii). 